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Showing metabocard for Cer(d18:1/24:1) (HMDB0004953)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-07-07 20:53:56 UTC
HMDB IDHMDB0004953
Secondary Accession Numbers
  • HMDB04953
Metabolite Identification
Common NameCer(d18:1/24:1)
DescriptionCer(d18:1/24:1(15Z)), also known as N-15Z-tetracosenoyl-sphing-4-enine, is a ceramide (Cer). Ceramides are members of the class of compounds known as sphingolipids (SPs), or glycosylceramides. SPs are lipids containing a backbone of sphingoid bases (e.g. sphingosine or sphinganine) that are often covalently bound to a fatty acid derivative through N-acylation. SPs are found in cell membranes, particularly in peripheral nerve cells and the cells found in the central nervous system (including the brain and spinal cord). Sphingolipids are extremely versatile molecules that have functions controlling fundamental cellular processes such as cell division, differentiation, and cell death. Impairments associated with sphingolipid metabolism are associated with many common human diseases such as diabetes, various cancers, microbial infections, diseases of the cardiovascular and respiratory systems, Alzheimer’s disease and other neurological syndromes. The biosynthesis and catabolism of sphingolipids involves a large number of intermediate metabolites where many different enzymes are involved. Simple sphingolipids, which include the sphingoid bases and ceramides, make up the early products of the sphingolipid synthetic pathways, while complex sphingolipids may be formed by the addition of head groups to the ceramide template (Wikipedia). In humans, ceramides are phosphorylated to ceramide phosphates (CerPs) through the action of a specific ceramide kinase (CerK). Ceramide phosphates are important metabolites of ceramides as they act as a mediators of the inflammatory response. Ceramides are also one of the hydrolysis byproducts of sphingomyelins (SMs) through the action of the enzyme sphingomyelin phosphodiesterase, which has been identified in the subcellular fractions of human epidermis (PMID: 25935 ) and many other tissues. Ceramides can also be synthesized from serine and palmitate in a de novo pathway and are regarded as important cellular signals for inducing apoptosis (PMID: 14998372 ). Ceramides are key in the biosynthesis of glycosphingolipids and gangliosides. In terms of its appearance and structure, Cer(d18:1/24:1(15Z)) is a colorless solid that consists of an unsaturated 18-carbon sphingoid base with an attached unsaturated 15Z-tetracosenoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481 ).
Structure
Data?1582752333
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0004953 (Cer(d18:1/24:1))


  Mrv1652304202019552D          

 46 45  0  0  1  0            999 V2000
   11.0930   -6.4511    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.8026   -6.8720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5219   -6.4679    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.2315   -6.8888    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.9507   -6.4847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6603   -6.9055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3796   -6.5014    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0892   -6.9223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8085   -6.5183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5180   -6.9391    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2373   -6.5350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9469   -6.9559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.6662   -6.5518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.3758   -6.9726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.0950   -6.5686    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.8047   -6.9895    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.5239   -6.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2335   -7.0063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2217   -7.7137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5316   -5.6429    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.2509   -5.2389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2606   -4.4139    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9584   -5.6632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6797   -5.2626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3872   -5.6869    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1084   -5.2863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8160   -5.7105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5372   -5.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2448   -5.7342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9660   -5.3336    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.6736   -5.7579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.3948   -5.3574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.1023   -5.7817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.8236   -5.3812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.5311   -5.8055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2396   -7.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2523   -5.4049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9599   -5.8292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9462   -6.6541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6629   -7.0626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.6677   -7.8876    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3844   -8.2961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3891   -9.1210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.1059   -9.5295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.1106  -10.3545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.8275  -10.7629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 13 12  1  0  0  0  0
 14 13  1  0  0  0  0
 15 14  1  0  0  0  0
 16 15  1  0  0  0  0
 17 16  1  0  0  0  0
 18 17  1  0  0  0  0
  4 19  1  1  0  0  0
  3 20  1  6  0  0  0
 22 21  2  0  0  0  0
 20 21  1  0  0  0  0
 23 21  1  0  0  0  0
 24 23  1  0  0  0  0
 25 24  1  0  0  0  0
 26 25  1  0  0  0  0
 27 26  1  0  0  0  0
 28 27  1  0  0  0  0
 29 28  1  0  0  0  0
 30 29  1  0  0  0  0
 31 30  1  0  0  0  0
 32 31  1  0  0  0  0
 33 32  1  0  0  0  0
 34 33  1  0  0  0  0
 35 34  1  0  0  0  0
 36 18  1  0  0  0  0
 37 35  1  0  0  0  0
 38 37  2  0  0  0  0
 39 38  1  0  0  0  0
 40 39  1  0  0  0  0
 41 40  1  0  0  0  0
 42 41  1  0  0  0  0
 43 42  1  0  0  0  0
 44 43  1  0  0  0  0
 45 44  1  0  0  0  0
 46 45  1  0  0  0  0
M  END
Download

3D MOL for HMDB0004953 (Cer(d18:1/24:1))

HMDB0004953
     RDKit          3D
Cer(d18:1/24:1(15Z))
127126  0  0  0  0  0  0  0  0999 V2000
   17.3690   -0.8451    0.0121 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4921    0.1837    1.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7908   -0.2099    2.3637 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2961   -0.4426    2.1570 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6476    0.7876    1.6116 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1722    0.7160    1.3710 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9022   -0.4440    0.4343 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4692   -0.5109    0.0247 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4706   -0.6026    1.0919 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5687    0.4167    1.2061 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6968    1.5201    0.2473 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6081    1.7614   -0.7105 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2854    2.1983   -0.3087 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4269    1.4942    0.6385 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0859    0.0683    0.3850 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5546   -0.1936   -0.9924 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1151   -1.6187   -1.1160 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8633   -1.8803   -0.2651 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8223   -0.9957   -0.8390 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4385   -1.0589   -0.3678 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1169   -0.7716    1.0523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4339   -0.8837    1.2269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1066    0.0946    0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6242   -0.0912    0.4477 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9942   -0.7830    1.4250 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3887    0.5214   -0.5463 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1282    1.1107   -1.5026 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1473    0.2701   -2.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8941    0.8686   -3.7897 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5197    1.6130   -1.2463 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.5648    2.5949   -0.2455 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4512    0.5049   -0.9756 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7392    0.7536   -0.7200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6936   -0.3346   -0.4406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3266   -0.1569    0.8993 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0090    1.0767    1.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1763    1.6559    0.5883 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3121    2.0912   -0.7874 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2326    1.3641   -2.0167 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0188    0.2954   -2.5479 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2086   -1.0143   -1.9897 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.9182   -1.1732   -0.6836 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.2999   -0.5714   -0.7659 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1284   -0.6778    0.4645 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.5973   -0.0143    1.6822 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.5982   -0.2281    2.8305 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6473   -1.6188    0.2362 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.9637   -0.3219   -0.9100 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.3611   -1.2379   -0.3025 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.5805    0.4025    1.2912 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.0806    1.1475    0.7367 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.8615    0.6559    3.0600 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.2899   -1.0723    2.7937 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.0743   -1.3564    1.5970 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8813   -0.6232    3.1898 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8310    1.6936    2.2611 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1124    1.0262    0.6093 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5888    0.5389    2.3007 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.8796    1.6489    0.8638 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.1224   -1.3670    1.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6021   -0.4522   -0.4208 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3473   -1.5579   -0.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2878    0.1522   -0.8058 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4091   -1.4283    1.7777 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8275    0.3402    1.9819 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7129    1.7275   -0.1396 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5985    2.4590    0.9747 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4785    0.8915   -1.4286 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0038    2.5640   -1.4276 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4225    3.2500    0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7161    2.4706   -1.2742 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8703    1.6127    1.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4420    2.0462    0.6762 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9602   -0.6409    0.5146 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3833   -0.2426    1.1841 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4100   -0.1016   -1.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8440    0.5675   -1.3614 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9063   -2.2646   -0.6876 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8649   -1.8849   -2.1779 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1110   -1.7095    0.7763 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5668   -2.9458   -0.4164 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1278    0.0949   -0.7562 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8091   -1.1948   -1.9588 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9618   -2.0450   -0.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8837   -0.2679   -0.9828 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5556   -1.4352    1.7954 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4070    0.2628    1.2919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7483   -1.9245    1.0654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6368   -0.6017    2.2817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9296    1.1605    0.6874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9212    0.0602   -0.7236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5225   -0.0228   -0.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6151    2.0974   -1.8948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1104    0.1114   -3.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6054   -0.7226   -2.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4155    0.7186   -4.6731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8586    2.0676   -2.2108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5281    3.4517   -0.6858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1080   -0.5177   -0.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0267    1.8088   -0.7326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3424   -0.6087   -1.2663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0296   -1.2727   -0.3118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4997   -0.3920    1.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0202   -1.0496    1.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1835    1.9028    1.2882 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2468    1.0140    2.3562 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0004953 (Cer(d18:1/24:1))


  Mrv1652304202019552D          

 46 45  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0004953

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCCC\C=C\[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCC\C=C/CCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C42H81NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h17-18,35,37,40-41,44-45H,3-16,19-34,36,38-39H2,1-2H3,(H,43,46)/b18-17-,37-35+/t40-,41+/m0/s1

> <INCHI_KEY>
VJSBNBBOSZJDKB-KPEYJIHVSA-N

> <FORMULA>
C42H81NO3

> <MOLECULAR_WEIGHT>
648.0974

> <EXACT_MASS>
647.621645463

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
127

> <JCHEM_AVERAGE_POLARIZABILITY>
88.77810552952155

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(15Z)-N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracos-15-enamide

> <ALOGPS_LOGP>
10.44

> <JCHEM_LOGP>
14.059982807000004

> <ALOGPS_LOGS>
-7.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.235174526465968

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.61974905944669

> <JCHEM_PKA_STRONGEST_BASIC>
-1.0489347908069546

> <JCHEM_POLAR_SURFACE_AREA>
69.56

> <JCHEM_REFRACTIVITY>
203.7003

> <JCHEM_ROTATABLE_BOND_COUNT>
37

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.80e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-(15Z-tetracosenoyl)-ceramide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0004953 (Cer(d18:1/24:1))

HMDB0004953
     RDKit          3D
Cer(d18:1/24:1(15Z))
127126  0  0  0  0  0  0  0  0999 V2000
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   13.1224   -1.3670    1.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6021   -0.4522   -0.4208 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3473   -1.5579   -0.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2878    0.1522   -0.8058 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4091   -1.4283    1.7777 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8275    0.3402    1.9819 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7129    1.7275   -0.1396 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5985    2.4590    0.9747 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4785    0.8915   -1.4286 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0038    2.5640   -1.4276 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4225    3.2500    0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7161    2.4706   -1.2742 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8703    1.6127    1.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4420    2.0462    0.6762 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9602   -0.6409    0.5146 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3833   -0.2426    1.1841 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4100   -0.1016   -1.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8440    0.5675   -1.3614 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9063   -2.2646   -0.6876 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8649   -1.8849   -2.1779 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1110   -1.7095    0.7763 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5668   -2.9458   -0.4164 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1278    0.0949   -0.7562 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8091   -1.1948   -1.9588 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9618   -2.0450   -0.6997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8837   -0.2679   -0.9828 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5556   -1.4352    1.7954 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4070    0.2628    1.2919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7483   -1.9245    1.0654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6368   -0.6017    2.2817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9296    1.1605    0.6874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9212    0.0602   -0.7236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5225   -0.0228   -0.0098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6151    2.0974   -1.8948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1104    0.1114   -3.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6054   -0.7226   -2.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4155    0.7186   -4.6731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8586    2.0676   -2.2108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5281    3.4517   -0.6858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1080   -0.5177   -0.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0267    1.8088   -0.7326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3424   -0.6087   -1.2663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0296   -1.2727   -0.3118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4997   -0.3920    1.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.1835    1.9028    1.2882 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2468    1.0140    2.3562 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1067    1.1310    0.9691 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3811    2.6816    1.2312 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2675    2.7977   -0.8355 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5259    2.9828   -0.9014 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3661    2.2490   -2.8761 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1217    1.1853   -2.2887 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5872    0.1154   -3.6382 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.0852    0.7163   -2.8267 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2560   -1.6449   -1.9955 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8490   -1.6385   -2.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3926   -0.8400    0.1832 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.0252   -2.3124   -0.5582 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.2293    0.4777   -1.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.8243   -1.1697   -1.5609 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.1252   -0.1901    0.2197 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.3368   -1.7552    0.7364 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6616   -0.5136    2.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.4729    1.0969    1.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8269   -1.3016    2.8449 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.1499    0.0563    3.7976 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5256    0.3555    2.6395 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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M  END
Download

PDB for HMDB0004953 (Cer(d18:1/24:1))

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  O   UNK     0      20.707 -12.042   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      22.032 -12.828   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      23.374 -12.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      24.699 -12.859   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      26.041 -12.105   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.366 -12.890   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      28.709 -12.136   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      30.033 -12.922   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      31.376 -12.167   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      32.700 -12.953   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      34.043 -12.199   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      35.368 -12.984   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      36.710 -12.230   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      38.035 -13.016   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      39.377 -12.261   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      40.702 -13.047   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      42.045 -12.293   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      43.369 -13.078   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      24.681 -14.399   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      23.392 -10.533   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      24.735  -9.779   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      24.753  -8.239   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      26.056 -10.571   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      27.402  -9.824   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      28.723 -10.616   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      30.069  -9.868   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      31.390 -10.660   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      32.736  -9.912   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      34.057 -10.704   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      35.403  -9.956   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      36.724 -10.748   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      38.070 -10.000   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      39.391 -10.793   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      40.737 -10.045   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      42.058 -10.837   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      43.381 -14.844   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      43.404 -10.089   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      44.725 -10.881   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      44.700 -12.421   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      46.037 -13.184   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      46.046 -14.724   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      47.384 -15.486   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      47.393 -17.026   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      48.731 -17.788   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      48.740 -19.328   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      50.078 -20.091   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   20                                                  
CONECT    4    3    5   19                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   36                                                       
CONECT   19    4                                                            
CONECT   20    3   21                                                       
CONECT   21   22   20   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   37                                                       
CONECT   36   18                                                            
CONECT   37   35   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45                                                            
MASTER        0    0    0    0    0    0    0    0   46    0   90    0
END
Download

3D PDB for HMDB0004953 (Cer(d18:1/24:1))

COMPND    HMDB0004953
HETATM    1  C1  UNL     1      17.369  -0.845   0.012  1.00  0.00           C  
HETATM    2  C2  UNL     1      17.492   0.184   1.083  1.00  0.00           C  
HETATM    3  C3  UNL     1      16.791  -0.210   2.364  1.00  0.00           C  
HETATM    4  C4  UNL     1      15.296  -0.443   2.157  1.00  0.00           C  
HETATM    5  C5  UNL     1      14.648   0.788   1.612  1.00  0.00           C  
HETATM    6  C6  UNL     1      13.172   0.716   1.371  1.00  0.00           C  
HETATM    7  C7  UNL     1      12.902  -0.444   0.434  1.00  0.00           C  
HETATM    8  C8  UNL     1      11.469  -0.511   0.025  1.00  0.00           C  
HETATM    9  C9  UNL     1      10.471  -0.603   1.092  1.00  0.00           C  
HETATM   10  C10 UNL     1       9.569   0.417   1.206  1.00  0.00           C  
HETATM   11  C11 UNL     1       9.697   1.520   0.247  1.00  0.00           C  
HETATM   12  C12 UNL     1       8.608   1.761  -0.711  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.285   2.198  -0.309  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.427   1.494   0.638  1.00  0.00           C  
HETATM   15  C15 UNL     1       6.086   0.068   0.385  1.00  0.00           C  
HETATM   16  C16 UNL     1       5.555  -0.194  -0.992  1.00  0.00           C  
HETATM   17  C17 UNL     1       5.115  -1.619  -1.116  1.00  0.00           C  
HETATM   18  C18 UNL     1       3.863  -1.880  -0.265  1.00  0.00           C  
HETATM   19  C19 UNL     1       2.822  -0.996  -0.839  1.00  0.00           C  
HETATM   20  C20 UNL     1       1.438  -1.059  -0.368  1.00  0.00           C  
HETATM   21  C21 UNL     1       1.117  -0.772   1.052  1.00  0.00           C  
HETATM   22  C22 UNL     1      -0.434  -0.884   1.227  1.00  0.00           C  
HETATM   23  C23 UNL     1      -1.107   0.095   0.341  1.00  0.00           C  
HETATM   24  C24 UNL     1      -2.624  -0.091   0.448  1.00  0.00           C  
HETATM   25  O1  UNL     1      -2.994  -0.783   1.425  1.00  0.00           O  
HETATM   26  N1  UNL     1      -3.389   0.521  -0.546  1.00  0.00           N  
HETATM   27  C25 UNL     1      -4.128   1.111  -1.503  1.00  0.00           C  
HETATM   28  C26 UNL     1      -4.147   0.270  -2.783  1.00  0.00           C  
HETATM   29  O2  UNL     1      -4.894   0.869  -3.790  1.00  0.00           O  
HETATM   30  C27 UNL     1      -5.520   1.613  -1.246  1.00  0.00           C  
HETATM   31  O3  UNL     1      -5.565   2.595  -0.245  1.00  0.00           O  
HETATM   32  C28 UNL     1      -6.451   0.505  -0.976  1.00  0.00           C  
HETATM   33  C29 UNL     1      -7.739   0.754  -0.720  1.00  0.00           C  
HETATM   34  C30 UNL     1      -8.694  -0.335  -0.441  1.00  0.00           C  
HETATM   35  C31 UNL     1      -9.327  -0.157   0.899  1.00  0.00           C  
HETATM   36  C32 UNL     1     -10.009   1.077   1.213  1.00  0.00           C  
HETATM   37  C33 UNL     1     -11.176   1.656   0.588  1.00  0.00           C  
HETATM   38  C34 UNL     1     -11.312   2.091  -0.787  1.00  0.00           C  
HETATM   39  C35 UNL     1     -11.233   1.364  -2.017  1.00  0.00           C  
HETATM   40  C36 UNL     1     -12.019   0.295  -2.548  1.00  0.00           C  
HETATM   41  C37 UNL     1     -12.209  -1.014  -1.990  1.00  0.00           C  
HETATM   42  C38 UNL     1     -12.918  -1.173  -0.684  1.00  0.00           C  
HETATM   43  C39 UNL     1     -14.300  -0.571  -0.766  1.00  0.00           C  
HETATM   44  C40 UNL     1     -15.128  -0.678   0.464  1.00  0.00           C  
HETATM   45  C41 UNL     1     -14.597  -0.014   1.682  1.00  0.00           C  
HETATM   46  C42 UNL     1     -15.598  -0.228   2.830  1.00  0.00           C  
HETATM   47  H1  UNL     1      16.647  -1.619   0.236  1.00  0.00           H  
HETATM   48  H2  UNL     1      16.964  -0.322  -0.910  1.00  0.00           H  
HETATM   49  H3  UNL     1      18.361  -1.238  -0.302  1.00  0.00           H  
HETATM   50  H4  UNL     1      18.580   0.403   1.291  1.00  0.00           H  
HETATM   51  H5  UNL     1      17.081   1.147   0.737  1.00  0.00           H  
HETATM   52  H6  UNL     1      16.862   0.656   3.060  1.00  0.00           H  
HETATM   53  H7  UNL     1      17.290  -1.072   2.794  1.00  0.00           H  
HETATM   54  H8  UNL     1      15.074  -1.356   1.597  1.00  0.00           H  
HETATM   55  H9  UNL     1      14.881  -0.623   3.190  1.00  0.00           H  
HETATM   56  H10 UNL     1      14.831   1.694   2.261  1.00  0.00           H  
HETATM   57  H11 UNL     1      15.112   1.026   0.609  1.00  0.00           H  
HETATM   58  H12 UNL     1      12.589   0.539   2.301  1.00  0.00           H  
HETATM   59  H13 UNL     1      12.880   1.649   0.864  1.00  0.00           H  
HETATM   60  H14 UNL     1      13.122  -1.367   1.023  1.00  0.00           H  
HETATM   61  H15 UNL     1      13.602  -0.452  -0.421  1.00  0.00           H  
HETATM   62  H16 UNL     1      11.347  -1.558  -0.518  1.00  0.00           H  
HETATM   63  H17 UNL     1      11.288   0.152  -0.806  1.00  0.00           H  
HETATM   64  H18 UNL     1      10.409  -1.428   1.778  1.00  0.00           H  
HETATM   65  H19 UNL     1       8.828   0.340   1.982  1.00  0.00           H  
HETATM   66  H20 UNL     1      10.713   1.728  -0.140  1.00  0.00           H  
HETATM   67  H21 UNL     1       9.599   2.459   0.975  1.00  0.00           H  
HETATM   68  H22 UNL     1       8.478   0.891  -1.429  1.00  0.00           H  
HETATM   69  H23 UNL     1       9.004   2.564  -1.428  1.00  0.00           H  
HETATM   70  H24 UNL     1       7.423   3.250   0.145  1.00  0.00           H  
HETATM   71  H25 UNL     1       6.716   2.471  -1.274  1.00  0.00           H  
HETATM   72  H26 UNL     1       6.870   1.613   1.671  1.00  0.00           H  
HETATM   73  H27 UNL     1       5.442   2.046   0.676  1.00  0.00           H  
HETATM   74  H28 UNL     1       6.960  -0.641   0.515  1.00  0.00           H  
HETATM   75  H29 UNL     1       5.383  -0.243   1.184  1.00  0.00           H  
HETATM   76  H30 UNL     1       6.410  -0.102  -1.761  1.00  0.00           H  
HETATM   77  H31 UNL     1       4.844   0.567  -1.361  1.00  0.00           H  
HETATM   78  H32 UNL     1       5.906  -2.265  -0.688  1.00  0.00           H  
HETATM   79  H33 UNL     1       4.865  -1.885  -2.178  1.00  0.00           H  
HETATM   80  H34 UNL     1       4.111  -1.710   0.776  1.00  0.00           H  
HETATM   81  H35 UNL     1       3.567  -2.946  -0.416  1.00  0.00           H  
HETATM   82  H36 UNL     1       3.128   0.095  -0.756  1.00  0.00           H  
HETATM   83  H37 UNL     1       2.809  -1.195  -1.959  1.00  0.00           H  
HETATM   84  H38 UNL     1       0.962  -2.045  -0.700  1.00  0.00           H  
HETATM   85  H39 UNL     1       0.884  -0.268  -0.983  1.00  0.00           H  
HETATM   86  H40 UNL     1       1.556  -1.435   1.795  1.00  0.00           H  
HETATM   87  H41 UNL     1       1.407   0.263   1.292  1.00  0.00           H  
HETATM   88  H42 UNL     1      -0.748  -1.924   1.065  1.00  0.00           H  
HETATM   89  H43 UNL     1      -0.637  -0.602   2.282  1.00  0.00           H  
HETATM   90  H44 UNL     1      -0.930   1.161   0.687  1.00  0.00           H  
HETATM   91  H45 UNL     1      -0.921   0.060  -0.724  1.00  0.00           H  
HETATM   92  H46 UNL     1      -4.522  -0.023  -0.010  1.00  0.00           H  
HETATM   93  H47 UNL     1      -3.615   2.097  -1.895  1.00  0.00           H  
HETATM   94  H48 UNL     1      -3.110   0.111  -3.086  1.00  0.00           H  
HETATM   95  H49 UNL     1      -4.605  -0.723  -2.532  1.00  0.00           H  
HETATM   96  H50 UNL     1      -4.416   0.719  -4.673  1.00  0.00           H  
HETATM   97  H51 UNL     1      -5.859   2.068  -2.211  1.00  0.00           H  
HETATM   98  H52 UNL     1      -5.528   3.452  -0.686  1.00  0.00           H  
HETATM   99  H53 UNL     1      -6.108  -0.518  -0.992  1.00  0.00           H  
HETATM  100  H54 UNL     1      -8.027   1.809  -0.733  1.00  0.00           H  
HETATM  101  H55 UNL     1      -9.342  -0.609  -1.266  1.00  0.00           H  
HETATM  102  H56 UNL     1      -8.030  -1.273  -0.312  1.00  0.00           H  
HETATM  103  H57 UNL     1      -8.500  -0.392   1.659  1.00  0.00           H  
HETATM  104  H58 UNL     1     -10.020  -1.050   1.020  1.00  0.00           H  
HETATM  105  H59 UNL     1      -9.184   1.903   1.288  1.00  0.00           H  
HETATM  106  H60 UNL     1     -10.247   1.014   2.356  1.00  0.00           H  
HETATM  107  H61 UNL     1     -12.107   1.131   0.969  1.00  0.00           H  
HETATM  108  H62 UNL     1     -11.381   2.682   1.231  1.00  0.00           H  
HETATM  109  H63 UNL     1     -12.268   2.798  -0.835  1.00  0.00           H  
HETATM  110  H64 UNL     1     -10.526   2.983  -0.901  1.00  0.00           H  
HETATM  111  H65 UNL     1     -11.366   2.249  -2.876  1.00  0.00           H  
HETATM  112  H66 UNL     1     -10.122   1.185  -2.289  1.00  0.00           H  
HETATM  113  H67 UNL     1     -11.587   0.115  -3.638  1.00  0.00           H  
HETATM  114  H68 UNL     1     -13.085   0.716  -2.827  1.00  0.00           H  
HETATM  115  H69 UNL     1     -11.256  -1.645  -1.995  1.00  0.00           H  
HETATM  116  H70 UNL     1     -12.849  -1.639  -2.747  1.00  0.00           H  
HETATM  117  H71 UNL     1     -12.393  -0.840   0.183  1.00  0.00           H  
HETATM  118  H72 UNL     1     -13.025  -2.312  -0.558  1.00  0.00           H  
HETATM  119  H73 UNL     1     -14.229   0.478  -1.169  1.00  0.00           H  
HETATM  120  H74 UNL     1     -14.824  -1.170  -1.561  1.00  0.00           H  
HETATM  121  H75 UNL     1     -16.125  -0.190   0.220  1.00  0.00           H  
HETATM  122  H76 UNL     1     -15.337  -1.755   0.736  1.00  0.00           H  
HETATM  123  H77 UNL     1     -13.662  -0.514   2.056  1.00  0.00           H  
HETATM  124  H78 UNL     1     -14.473   1.097   1.601  1.00  0.00           H  
HETATM  125  H79 UNL     1     -15.827  -1.302   2.845  1.00  0.00           H  
HETATM  126  H80 UNL     1     -15.150   0.056   3.798  1.00  0.00           H  
HETATM  127  H81 UNL     1     -16.526   0.356   2.640  1.00  0.00           H  
CONECT    1    2   47   48   49
CONECT    2    3   50   51
CONECT    3    4   52   53
CONECT    4    5   54   55
CONECT    5    6   56   57
CONECT    6    7   58   59
CONECT    7    8   60   61
CONECT    8    9   62   63
CONECT    9   10   10   64
CONECT   10   11   65
CONECT   11   12   66   67
CONECT   12   13   68   69
CONECT   13   14   70   71
CONECT   14   15   72   73
CONECT   15   16   74   75
CONECT   16   17   76   77
CONECT   17   18   78   79
CONECT   18   19   80   81
CONECT   19   20   82   83
CONECT   20   21   84   85
CONECT   21   22   86   87
CONECT   22   23   88   89
CONECT   23   24   90   91
CONECT   24   25   25   26
CONECT   26   27   92
CONECT   27   28   30   93
CONECT   28   29   94   95
CONECT   29   96
CONECT   30   31   32   97
CONECT   31   98
CONECT   32   33   33   99
CONECT   33   34  100
CONECT   34   35  101  102
CONECT   35   36  103  104
CONECT   36   37  105  106
CONECT   37   38  107  108
CONECT   38   39  109  110
CONECT   39   40  111  112
CONECT   40   41  113  114
CONECT   41   42  115  116
CONECT   42   43  117  118
CONECT   43   44  119  120
CONECT   44   45  121  122
CONECT   45   46  123  124
CONECT   46  125  126  127
END
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SMILES for HMDB0004953 (Cer(d18:1/24:1))

CCCCCCCCCCCCC\C=C\[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCC\C=C/CCCCCCCC
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INCHI for HMDB0004953 (Cer(d18:1/24:1))

InChI=1S/C42H81NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h17-18,35,37,40-41,44-45H,3-16,19-34,36,38-39H2,1-2H3,(H,43,46)/b18-17-,37-35+/t40-,41+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
C24:1 CerChEBI
Ceramide (D18:1/24:1(15Z))ChEBI
N-(15-cis)-TetracosenoylsphingosineChEBI
N-(15Z-Tetracosenoyl)-sphing-4-enineChEBI
N-(15Z-Tetracosenoyl)ceramideChEBI
N-(15Z-Tetracosenoyl)sphing-4-enineChEBI
N-NervonylsphingosineChEBI
(2S,3R,4E)-2-Acylamino-1,3-octadec-4-enediolHMDB
(2S,3R,4E)-2-Acylaminooctadec-4-ene-1,3-diolHMDB
CerHMDB
CeramideHMDB
N-AcylsphingosineHMDB
N-[(1S,2R,3E)-2-Hydroxy-1-(hydroxymethyl)-3-heptadecenyl]-octadecanamideHMDB
Ceramide(D18:1/24:1(15Z))HMDB
N-(15Z-Tetracosenoyl)-sphingosineHMDB
N-(15Z-Tetracosenoyl)-D-erythro-sphingosineHMDB
N-(15Z-Tetracosenoyl)-4-sphingenineHMDB
N-(15Z-Tetracosenoyl)-D-sphingosineHMDB
N-(15Z-Tetracosenoyl)-sphingenineHMDB
N-(15Z-Tetracosenoyl)-erythro-4-sphingenineHMDB
Cer(D18:1/24:1(15Z))ChEBI
Chemical FormulaC42H81NO3
Average Molecular Weight648.0974
Monoisotopic Molecular Weight647.621645463
IUPAC Name(15Z)-N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracos-15-enamide
Traditional NameN-(15Z-tetracosenoyl)-ceramide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCC\C=C\[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C42H81NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h17-18,35,37,40-41,44-45H,3-16,19-34,36,38-39H2,1-2H3,(H,43,46)/b18-17-,37-35+/t40-,41+/m0/s1
InChI KeyVJSBNBBOSZJDKB-KPEYJIHVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ceramides. These are lipid molecules containing a sphingosine in which the amine group is linked to a fatty acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassCeramides
Direct ParentCeramides
Alternative Parents
Substituents
  • Ceramide
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Carboxamide group
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Carboxylic acid derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0Not Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.8e-05 g/LALOGPS
logP10.44ALOGPS
logP14.06ChemAxon
logS-7.6ALOGPS
pKa (Strongest Acidic)13.62ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count37ChemAxon
Refractivity203.7 m³·mol⁻¹ChemAxon
Polarizability88.78 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+272.42131661259
DarkChem[M-H]-263.72731661259
DeepCCS[M+H]+274.77530932474
DeepCCS[M-H]-272.3830932474
DeepCCS[M-2H]-305.26430932474
DeepCCS[M+Na]+280.68830932474
AllCCS[M+H]+278.032859911
AllCCS[M+H-H2O]+277.632859911
AllCCS[M+NH4]+278.432859911
AllCCS[M+Na]+278.532859911
AllCCS[M-H]-263.732859911
AllCCS[M+Na-2H]-269.032859911
AllCCS[M+HCOO]-275.032859911

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Cer(d18:1/24:1(15Z)),1TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C5023.3Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),1TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C4606.6Standard non polar33892256
Cer(d18:1/24:1(15Z)),1TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C5022.2Standard polar33892256
Cer(d18:1/24:1(15Z)),1TMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC4999.2Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),1TMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC4677.7Standard non polar33892256
Cer(d18:1/24:1(15Z)),1TMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC5285.6Standard polar33892256
Cer(d18:1/24:1(15Z)),1TMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C4852.3Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),1TMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C4641.2Standard non polar33892256
Cer(d18:1/24:1(15Z)),1TMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C5308.6Standard polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C4946.3Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C4483.3Standard non polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C4691.1Standard polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4833.8Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4493.9Standard non polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4759.6Standard polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C4807.6Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C4555.3Standard non polar33892256
Cer(d18:1/24:1(15Z)),2TMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C5022.4Standard polar33892256
Cer(d18:1/24:1(15Z)),3TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4817.6Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),3TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4486.9Standard non polar33892256
Cer(d18:1/24:1(15Z)),3TMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4488.9Standard polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C5243.2Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C4698.0Standard non polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C5019.5Standard polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C(C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC5237.0Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C(C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC4779.7Standard non polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C(C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC5252.8Standard polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C5078.5Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C4738.0Standard non polar33892256
Cer(d18:1/24:1(15Z)),1TBDMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C5265.3Standard polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C(C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C5433.4Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C(C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C4714.9Standard non polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #1CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N[C@@H](CO[Si](C)(C)C(C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C4773.5Standard polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C5290.7Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C4736.8Standard non polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #2CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C4839.8Standard polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C(C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C5268.8Semi standard non polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C(C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C4778.8Standard non polar33892256
Cer(d18:1/24:1(15Z)),2TBDMS,isomer #3CCCCCCCC/C=C\CCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C(C)(C)C)[C@H](O)/C=C/CCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C5058.6Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:1/24:1) GC-MS (TMS_3_1) - 70eV, PositiveNot Available2022-08-08Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 10V, Positive-QTOFsplash10-0002-0000009000-1f40f0f6aabd3d3778222017-10-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 20V, Positive-QTOFsplash10-01ot-0050009000-2c2c621fcd34db4a00c62017-10-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 40V, Positive-QTOFsplash10-01q9-0090006000-76fbd24c138f61a26c692017-10-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 10V, Positive-QTOFsplash10-0udi-0000009000-31264534e837f791da652021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 20V, Positive-QTOFsplash10-0udi-0000009000-31264534e837f791da652021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 40V, Positive-QTOFsplash10-000i-0000009000-68b46d0682c146d495b72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 10V, Negative-QTOFsplash10-0002-0000009000-99b30254d9b8ff6d778b2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 20V, Negative-QTOFsplash10-0002-0010009000-e0f0fb15548876ff5fcc2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 40V, Negative-QTOFsplash10-01ot-0022009000-9cde7a2c939063482b602021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 10V, Positive-QTOFsplash10-0002-0000009000-8034b399a95d3586d3662021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 20V, Positive-QTOFsplash10-01ot-0050009000-60034ad5862116f2cc772021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:1/24:1) 40V, Positive-QTOFsplash10-01q9-0090006000-6bfbef23ab00b1bb555b2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Feces
Tissue Locations
  • Brain
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Neuron
  • Pancreas
  • Placenta
  • Platelet
  • Skeletal Muscle
  • Spleen
  • Testis
  • Thyroid Gland
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1 +/- 0.029 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023540
KNApSAcK IDNot Available
Chemspider ID4446681
KEGG Compound IDC00195
BioCyc IDCERAMIDE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID7206
PubChem Compound5283568
PDB IDNot Available
ChEBI ID74450
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Erdreich-Epstein A, Tran LB, Cox OT, Huang EY, Laug WE, Shimada H, Millard M: Endothelial apoptosis induced by inhibition of integrins alphavbeta3 and alphavbeta5 involves ceramide metabolic pathways. Blood. 2005 Jun 1;105(11):4353-61. Epub 2005 Feb 10. [PubMed:15705795 ]
  2. Guchhait P, Lopez JA, Thiagarajan P: Characterization of autoantibodies against sulfatide from a V-gene phage-display library derived from patients with systemic lupus erythematosus. J Immunol Methods. 2004 Dec;295(1-2):129-37. Epub 2004 Oct 26. [PubMed:15627618 ]
  3. Ogawa-Goto K, Ohta Y, Kubota K, Funamoto N, Abe T, Taki T, Nagashima K: Glycosphingolipids of human peripheral nervous system myelins isolated from cauda equina. J Neurochem. 1993 Oct;61(4):1398-403. [PubMed:7690848 ]
  4. Deguchi H, Yegneswaran S, Griffin JH: Sphingolipids as bioactive regulators of thrombin generation. J Biol Chem. 2004 Mar 26;279(13):12036-42. Epub 2004 Jan 13. [PubMed:14722105 ]
  5. Holleran WM, Ginns EI, Menon GK, Grundmann JU, Fartasch M, McKinney CE, Elias PM, Sidransky E: Consequences of beta-glucocerebrosidase deficiency in epidermis. Ultrastructure and permeability barrier alterations in Gaucher disease. J Clin Invest. 1994 Apr;93(4):1756-64. [PubMed:8163674 ]
  6. Saito M, Saito M, Cooper TB, Vadasz C: Ethanol-induced changes in the content of triglycerides, ceramides, and glucosylceramides in cultured neurons. Alcohol Clin Exp Res. 2005 Aug;29(8):1374-83. [PubMed:16131844 ]
  7. Garcia-Ruiz C, Mari M, Morales A, Colell A, Ardite E, Fernandez-Checa JC: Human placenta sphingomyelinase, an exogenous acidic pH-optimum sphingomyelinase, induces oxidative stress, glutathione depletion, and apoptosis in rat hepatocytes. Hepatology. 2000 Jul;32(1):56-65. [PubMed:10869289 ]
  8. van Lijnschoten G, Groener JE, Maas SM, Ben-Yoseph Y, Dingemans KP, Offerhaus GJ: Intrauterine fetal death due to Farber disease: case report. Pediatr Dev Pathol. 2000 Nov-Dec;3(6):597-602. [PubMed:11000338 ]
  9. Maurer BJ, Melton L, Billups C, Cabot MC, Reynolds CP: Synergistic cytotoxicity in solid tumor cell lines between N-(4-hydroxyphenyl)retinamide and modulators of ceramide metabolism. J Natl Cancer Inst. 2000 Dec 6;92(23):1897-909. [PubMed:11106681 ]
  10. Poliak S, Gollan L, Salomon D, Berglund EO, Ohara R, Ranscht B, Peles E: Localization of Caspr2 in myelinated nerves depends on axon-glia interactions and the generation of barriers along the axon. J Neurosci. 2001 Oct 1;21(19):7568-75. [PubMed:11567047 ]
  11. Kirby RJ, Zheng S, Tso P, Howles PN, Hui DY: Bile salt-stimulated carboxyl ester lipase influences lipoprotein assembly and secretion in intestine: a process mediated via ceramide hydrolysis. J Biol Chem. 2002 Feb 8;277(6):4104-9. Epub 2001 Dec 3. [PubMed:11733511 ]
  12. Bouwstra JA, Honeywell-Nguyen PL, Gooris GS, Ponec M: Structure of the skin barrier and its modulation by vesicular formulations. Prog Lipid Res. 2003 Jan;42(1):1-36. [PubMed:12467638 ]
  13. Adams JM 2nd, Pratipanawatr T, Berria R, Wang E, DeFronzo RA, Sullards MC, Mandarino LJ: Ceramide content is increased in skeletal muscle from obese insulin-resistant humans. Diabetes. 2004 Jan;53(1):25-31. [PubMed:14693694 ]
  14. Mari M, Colell A, Morales A, Paneda C, Varela-Nieto I, Garcia-Ruiz C, Fernandez-Checa JC: Acidic sphingomyelinase downregulates the liver-specific methionine adenosyltransferase 1A, contributing to tumor necrosis factor-induced lethal hepatitis. J Clin Invest. 2004 Mar;113(6):895-904. [PubMed:15067322 ]
  15. Helge JW, Dobrzyn A, Saltin B, Gorski J: Exercise and training effects on ceramide metabolism in human skeletal muscle. Exp Physiol. 2004 Jan;89(1):119-27. [PubMed:15109217 ]
  16. Jana A, Pahan K: Human immunodeficiency virus type 1 gp120 induces apoptosis in human primary neurons through redox-regulated activation of neutral sphingomyelinase. J Neurosci. 2004 Oct 27;24(43):9531-40. [PubMed:15509740 ]
  17. Yatomi Y, Yamamura S, Hisano N, Nakahara K, Igarashi Y, Ozaki Y: Sphingosine 1-phosphate breakdown in platelets. J Biochem. 2004 Oct;136(4):495-502. [PubMed:15625319 ]
  18. Chavez JA, Holland WL, Bar J, Sandhoff K, Summers SA: Acid ceramidase overexpression prevents the inhibitory effects of saturated fatty acids on insulin signaling. J Biol Chem. 2005 May 20;280(20):20148-53. Epub 2005 Mar 17. [PubMed:15774472 ]
  19. Petrache I, Natarajan V, Zhen L, Medler TR, Richter AT, Cho C, Hubbard WC, Berdyshev EV, Tuder RM: Ceramide upregulation causes pulmonary cell apoptosis and emphysema-like disease in mice. Nat Med. 2005 May;11(5):491-8. Epub 2005 Apr 24. [PubMed:15852018 ]
  20. Demarchi F, Bertoli C, Greer PA, Schneider C: Ceramide triggers an NF-kappaB-dependent survival pathway through calpain. Cell Death Differ. 2005 May;12(5):512-22. [PubMed:15933726 ]
  21. Klein J: Functions and pathophysiological roles of phospholipase D in the brain. J Neurochem. 2005 Sep;94(6):1473-87. Epub 2005 Jul 22. [PubMed:16042758 ]
  22. Ogawa-Goto K, Funamoto N, Abe T, Nagashima K: Different ceramide compositions of gangliosides between human motor and sensory nerves. J Neurochem. 1990 Nov;55(5):1486-93. [PubMed:2213006 ]
  23. Ghadially R, Brown BE, Sequeira-Martin SM, Feingold KR, Elias PM: The aged epidermal permeability barrier. Structural, functional, and lipid biochemical abnormalities in humans and a senescent murine model. J Clin Invest. 1995 May;95(5):2281-90. [PubMed:7738193 ]
  24. Marchesini S, Demasi L, Cestone P, Preti A, Agmon V, Dagan A, Navon R, Gatt S: Sulforhodamine GM1-ganglioside: synthesis and physicochemical properties. Chem Phys Lipids. 1994 Aug 8;72(2):143-52. [PubMed:7954976 ]
  25. Tojo K, Oota M, Honda H, Shibasaki T, Sakai O: Possible thyroidal involvement in a case of Fabry disease. Intern Med. 1994 Mar;33(3):172-6. [PubMed:8061397 ]
  26. Schafer A, Harzer K, Kattner E, Schafer HJ, Stoltenburg G, Lietz H: [Disseminated lipogranulomatosis (Farber disease) with hydrops fetalis]. Pathologe. 1996 Mar;17(2):145-9. [PubMed:8650144 ]
  27. Sando GN, Howard EJ, Madison KC: Induction of ceramide glucosyltransferase activity in cultured human keratinocytes. Correlation with culture differentiation. J Biol Chem. 1996 Sep 6;271(36):22044-51. [PubMed:8703011 ]
  28. Dunn HG, Dolman CL, Farrell DF, Tischler B, Hasinoff C, Woolf LI: Krabbe's leukodystrophy without globoid cells. Neurology. 1976 Nov;26(11):1035-41. [PubMed:988509 ]
  29. Bowser PA, Gray GM: Sphingomyelinase in pig and human epidermis. J Invest Dermatol. 1978 Jun;70(6):331-5. [PubMed:25935 ]
  30. Watanabe R, Wu K, Paul P, Marks DL, Kobayashi T, Pittelkow MR, Pagano RE: Up-regulation of glucosylceramide synthase expression and activity during human keratinocyte differentiation. J Biol Chem. 1998 Apr 17;273(16):9651-5. [PubMed:9545298 ]
  31. Ohnishi Y, Okino N, Ito M, Imayama S: Ceramidase activity in bacterial skin flora as a possible cause of ceramide deficiency in atopic dermatitis. Clin Diagn Lab Immunol. 1999 Jan;6(1):101-4. [PubMed:9874672 ]
  32. Humbert P: [Functional consequences of cutaneous lipid perturbation]. Pathol Biol (Paris). 2003 Jul;51(5):271-4. [PubMed:14567193 ]
  33. Cho Y, Lew BL, Seong K, Kim NI: An inverse relationship between ceramide synthesis and clinical severity in patients with psoriasis. J Korean Med Sci. 2004 Dec;19(6):859-63. [PubMed:15608398 ]
  34. Uchida Y, Behne M, Quiec D, Elias PM, Holleran WM: Vitamin C stimulates sphingolipid production and markers of barrier formation in submerged human keratinocyte cultures. J Invest Dermatol. 2001 Nov;117(5):1307-13. [PubMed:11710949 ]
  35. Pettus BJ, Baes M, Busman M, Hannun YA, Van Veldhoven PP: Mass spectrometric analysis of ceramide perturbations in brain and fibroblasts of mice and human patients with peroxisomal disorders. Rapid Commun Mass Spectrom. 2004;18(14):1569-74. [PubMed:15282781 ]
  36. Okamoto R, Arikawa J, Ishibashi M, Kawashima M, Takagi Y, Imokawa G: Sphingosylphosphorylcholine is upregulated in the stratum corneum of patients with atopic dermatitis. J Lipid Res. 2003 Jan;44(1):93-102. [PubMed:12518027 ]
  37. Lew BL, Cho Y, Kim J, Sim WY, Kim NI: Ceramides and cell signaling molecules in psoriatic epidermis: reduced levels of ceramides, PKC-alpha, and JNK. J Korean Med Sci. 2006 Feb;21(1):95-9. [PubMed:16479073 ]
  38. Grether-Beck S, Bonizzi G, Schmitt-Brenden H, Felsner I, Timmer A, Sies H, Johnson JP, Piette J, Krutmann J: Non-enzymatic triggering of the ceramide signalling cascade by solar UVA radiation. EMBO J. 2000 Nov 1;19(21):5793-800. [PubMed:11060030 ]
  39. Satoi H, Tomimoto H, Ohtani R, Kitano T, Kondo T, Watanabe M, Oka N, Akiguchi I, Furuya S, Hirabayashi Y, Okazaki T: Astroglial expression of ceramide in Alzheimer's disease brains: a role during neuronal apoptosis. Neuroscience. 2005;130(3):657-66. [PubMed:15590150 ]
  40. Gill JS, Windebank AJ: Suramin induced ceramide accumulation leads to apoptotic cell death in dorsal root ganglion neurons. Cell Death Differ. 1998 Oct;5(10):876-83. [PubMed:10203686 ]
  41. Both DM, Goodtzova K, Yarosh DB, Brown DA: Liposome-encapsulated ursolic acid increases ceramides and collagen in human skin cells. Arch Dermatol Res. 2002 Jan;293(11):569-75. [PubMed:11876525 ]
  42. Yarosh DB, Both D, Brown D: Liposomal ursolic acid (merotaine) increases ceramides and collagen in human skin. Horm Res. 2000;54(5-6):318-21. [PubMed:11595826 ]
  43. Persaud-Sawin DA, Boustany RM: Cell death pathways in juvenile Batten disease. Apoptosis. 2005 Oct;10(5):973-85. [PubMed:16151633 ]
  44. Di Marzio L, Cinque B, De Simone C, Cifone MG: Effect of the lactic acid bacterium Streptococcus thermophilus on ceramide levels in human keratinocytes in vitro and stratum corneum in vivo. J Invest Dermatol. 1999 Jul;113(1):98-106. [PubMed:10417626 ]
  45. Tanno O, Ota Y, Kitamura N, Katsube T, Inoue S: Nicotinamide increases biosynthesis of ceramides as well as other stratum corneum lipids to improve the epidermal permeability barrier. Br J Dermatol. 2000 Sep;143(3):524-31. [PubMed:10971324 ]
  46. Malagarie-Cazenave S, Segui B, Leveque S, Garcia V, Carpentier S, Altie MF, Brouchet A, Gouaze V, Andrieu-Abadie N, Barreira Y, Benoist H, Levade T: Role of FAN in tumor necrosis factor-alpha and lipopolysaccharide-induced interleukin-6 secretion and lethality in D-galactosamine-sensitized mice. J Biol Chem. 2004 Apr 30;279(18):18648-55. Epub 2004 Feb 25. [PubMed:14985352 ]
  47. Farina F, Cappello F, Todaro M, Bucchieri F, Peri G, Zummo G, Stassi G: Involvement of caspase-3 and GD3 ganglioside in ceramide-induced apoptosis in Farber disease. J Histochem Cytochem. 2000 Jan;48(1):57-62. [PubMed:10653586 ]
  48. Sugiki H, Hozumi Y, Maeshima H, Katagata Y, Mitsuhashi Y, Kondo S: C2-ceramide induces apoptosis in a human squamous cell carcinoma cell line. Br J Dermatol. 2000 Dec;143(6):1154-63. [PubMed:11122015 ]
  49. Lee HK, Nam GW, Kim SH, Lee SH: Phytocomponents of triterpenoids, oleanolic acid and ursolic acid, regulated differently the processing of epidermal keratinocytes via PPAR-alpha pathway. Exp Dermatol. 2006 Jan;15(1):66-73. [PubMed:16364033 ]
  50. Di Marzio L, Centi C, Cinque B, Masci S, Giuliani M, Arcieri A, Zicari L, De Simone C, Cifone MG: Effect of the lactic acid bacterium Streptococcus thermophilus on stratum corneum ceramide levels and signs and symptoms of atopic dermatitis patients. Exp Dermatol. 2003 Oct;12(5):615-20. [PubMed:14705802 ]
  51. Bektas M, Orfanos CE, Geilen CC: Different vitamin D analogues induce sphingomyelin hydrolysis and apoptosis in the human keratinocyte cell line HaCaT. Cell Mol Biol (Noisy-le-grand). 2000 Feb;46(1):111-9. [PubMed:10726977 ]
  52. Herr I, Martin-Villalba A, Kurz E, Roncaioli P, Schenkel J, Cifone MG, Debatin KM: FK506 prevents stroke-induced generation of ceramide and apoptosis signaling. Brain Res. 1999 May 1;826(2):210-9. [PubMed:10224298 ]
  53. Futerman AH: The roles of ceramide in the regulation of neuronal growth and development. Biochemistry (Mosc). 1998 Jan;63(1):74-83. [PubMed:9526098 ]
  54. Vielhaber G, Pfeiffer S, Brade L, Lindner B, Goldmann T, Vollmer E, Hintze U, Wittern KP, Wepf R: Localization of ceramide and glucosylceramide in human epidermis by immunogold electron microscopy. J Invest Dermatol. 2001 Nov;117(5):1126-36. [PubMed:11710923 ]
  55. Tserng KY, Griffin RL: Ceramide metabolite, not intact ceramide molecule, may be responsible for cellular toxicity. Biochem J. 2004 Jun 15;380(Pt 3):715-22. [PubMed:14998372 ]

Only showing the first 10 proteins. There are 70 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Lipid phosphate phosphohydrolase 2
General function:
Involved in catalytic activity
Specific function:
Catalyzes the conversion of phosphatidic acid (PA) to diacylglycerol (DG). In addition it hydrolyzes lysophosphatidic acid (LPA), ceramide-1-phosphate (C-1-P) and sphingosine-1-phosphate (S-1-P). The relative catalytic efficiency is PA > C-1-P > LPA > S-1-P.
Gene Name:
PPAP2C
Uniprot ID:
O43688
Molecular weight:
32573.435
Enzyme Details
2. Lipid phosphate phosphohydrolase 1
General function:
Involved in catalytic activity
Specific function:
Broad-specificity phosphohydrolase that dephosphorylates exogenous bioactive glycerolipids and sphingolipids. Catalyzes the conversion of phosphatidic acid (PA) to diacylglycerol (DG). Pivotal regulator of lysophosphatidic acid (LPA) signaling in the cardiovascular system. Major enzyme responsible of dephosphorylating LPA in platelets, which terminates signaling actions of LPA. May control circulating, and possibly also regulate localized, LPA levels resulting from platelet activation. It has little activity towards ceramide-1-phosphate (C-1-P) and sphingosine-1-phosphate (S-1-P). The relative catalytic efficiency is LPA > PA > S-1-P > C-1-P. It's down-regulation may contribute to the development of colon adenocarcinoma.
Gene Name:
PPAP2A
Uniprot ID:
O14494
Molecular weight:
32155.715
Enzyme Details
3. Lipid phosphate phosphohydrolase 3
General function:
Involved in catalytic activity
Specific function:
Catalyzes the conversion of phosphatidic acid (PA) to diacylglycerol (DG). In addition it hydrolyzes lysophosphatidic acid (LPA), ceramide-1-phosphate (C-1-P) and sphingosine-1-phosphate (S-1-P). The relative catalytic efficiency is LPA = PA > C-1-P > S-1-P. May be involved in cell adhesion and in cell-cell interactions.
Gene Name:
PPAP2B
Uniprot ID:
O14495
Molecular weight:
35115.61
Enzyme Details
4. Galactocerebrosidase
General function:
Involved in galactosylceramidase activity
Specific function:
Hydrolyzes the galactose ester bonds of galactosylceramide, galactosylsphingosine, lactosylceramide, and monogalactosyldiglyceride. Enzyme with very low activity responsible for the lysosomal catabolism of galactosylceramide, a major lipid in myelin, kidney and epithelial cells of small intestine and colon.
Gene Name:
GALC
Uniprot ID:
P54803
Molecular weight:
77062.86
Enzyme Details
5. Lactase-phlorizin hydrolase
General function:
Involved in hydrolase activity, hydrolyzing O-glycosyl compounds
Specific function:
LPH splits lactose in the small intestine.
Gene Name:
LCT
Uniprot ID:
P09848
Molecular weight:
218584.77
Enzyme Details
6. Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens
Gene Name:
GBGT1
Uniprot ID:
Q8N5D6
Molecular weight:
40126.9
Enzyme Details
7. N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase
General function:
Involved in N-acetylglucosaminylphosphatidylinositol de
Specific function:
Involved in the second step of GPI biosynthesis. De-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
Gene Name:
PIGL
Uniprot ID:
Q9Y2B2
Molecular weight:
28530.965
Enzyme Details
8. Phosphatidylcholine:ceramide cholinephosphotransferase 2
General function:
Involved in catalytic activity
Specific function:
Bidirectional lipid cholinephosphotransferase capable of converting phosphatidylcholine (PC) and ceramide to sphingomyelin (SM) and diacylglycerol (DAG) and vice versa. Direction is dependent on the relative concentrations of DAG and ceramide as phosphocholine acceptors. Directly and specifically recognizes the choline head group on the substrate. Also requires two fatty chains on the choline-P donor molecule in order to be recognized efficiently as a substrate. Does not function strictly as a SM synthase. Required for cell growth
Gene Name:
SGMS2
Uniprot ID:
Q8NHU3
Molecular weight:
42279.8
Enzyme Details
9. Phosphatidylcholine:ceramide cholinephosphotransferase 1
General function:
Involved in catalytic activity
Specific function:
Bidirectional lipid cholinephosphotransferase capable of converting phosphatidylcholine (PC) and ceramide to sphingomyelin (SM) and diacylglycerol (DAG) and vice versa. Direction is dependent on the relative concentrations of DAG and ceramide as phosphocholine acceptors. Directly and specifically recognizes the choline head group on the substrate. Also requires two fatty chains on the choline-P donor molecule in order to be recognized efficiently as a substrate. Does not function strictly as a SM synthase. Suppresses BAX-mediated apoptosis and also prevents cell death in response to stimuli such as hydrogen peroxide, osmotic stress, elevated temperature and exogenously supplied sphingolipids. May protect against cell death by reversing the stress-inducible increase in levels of proapoptotic ceramide. Required for cell growth
Gene Name:
SGMS1
Uniprot ID:
Q86VZ5
Molecular weight:
49207.3
Enzyme Details
10. Sphingomyelin phosphodiesterase
General function:
Involved in hydrolase activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost catalytic activity.
Gene Name:
SMPD1
Uniprot ID:
P17405
Molecular weight:
69935.53

Only showing the first 10 proteins. There are 70 proteins in total.

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