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Showing metabocard for Cer(d18:0/25:0) (HMDB0011770)

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enzymes (66) Show 66 proteins
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-03-24 16:16:38 UTC
Update Date2022-11-30 19:04:01 UTC
HMDB IDHMDB0011770
Secondary Accession Numbers
  • HMDB11770
Metabolite Identification
Common NameCer(d18:0/25:0)
DescriptionCer(d18:0/25:0), also known as N-pentacosanoyl-sphinganine, 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(d18:0/25:0) is a colorless solid that consists of a saturated 18-carbon sphingoid base with an attached saturated pentacosanoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481 ).
Structure
Data?1582752949
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011770 (Cer(d18:0/25:0))


  Mrv0541 02241201542D          

 47 46  0  0  1  0            999 V2000
   20.8179   -3.3315    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0988   -2.9270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3889   -3.3474    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.6699   -2.9429    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.9600   -3.3634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2410   -2.9589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5312   -3.3794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8120   -2.9749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1022   -3.3954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3832   -2.9909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6734   -3.4114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9543   -3.0069    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2444   -3.4273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5254   -3.0229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8156   -3.4433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0965   -3.0388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3867   -3.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6676   -3.0548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6607   -2.1179    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3982   -4.1724    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9577   -3.4752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2507   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9653   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6797   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3942   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1087   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8231   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5376   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2520   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9665   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6811   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3955   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1099   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8244   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5389   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2533   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9679   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6823   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3968   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1113   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8258   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5402   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2548   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.9692   -4.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6837   -4.5849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6837   -5.4099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5363   -4.5849    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  1  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
 21 18  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
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 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
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 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  1  0  0  0  0
 45 20  1  0  0  0  0
 45 46  2  0  0  0  0
 47 22  1  0  0  0  0
M  END
Download

3D MOL for HMDB0011770 (Cer(d18:0/25:0))

HMDB0011770
     RDKit          3D
Cer(d18:0/25:0)
134133  0  0  0  0  0  0  0  0999 V2000
   15.8838    0.8740    1.5817 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4474    0.6484    0.1935 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3012   -0.5461    0.0876 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8067   -1.8757    0.4261 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7271   -2.5610   -0.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4265   -1.8600   -0.2519 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3186   -2.6754   -0.9361 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0718   -1.8118   -0.8956 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6242   -1.4365    0.4715 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4036   -0.5000    0.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2997   -1.1959   -0.3523 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0926   -0.2204   -0.4585 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4868    0.9088   -1.3033 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6191    2.0540   -1.5630 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2831    1.9350   -2.1365 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2741    1.3037   -1.2181 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9631    1.3132   -1.9892 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7922    0.7908   -1.1805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5759    1.6567    0.0520 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3554    3.0971   -0.3456 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2077    3.3599   -1.2270 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1459    3.0276   -0.5903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2594    3.2796   -1.5487 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5850    3.0596   -0.9237 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8790    1.7341   -0.3788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0464    0.8256   -0.3786 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1789    1.4574    0.1841 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5957    0.2221    0.7613 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.9403    0.2866    2.2141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3016   -0.9470    2.7379 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5671   -0.5728   -0.0976 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.7699   -0.9395   -1.2988 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6614    0.2171   -0.6708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6375    0.9359    0.0834 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7366    0.5210    0.9242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6721   -0.3451    2.0978 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3932   -1.7934    1.9257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4743   -2.4867    1.0915 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8184   -2.3943    1.7837 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8615   -3.0984    0.9656 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0888   -2.5209   -0.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.5633   -1.1044   -0.3012 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.8846   -1.0837    0.4701 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.4104    0.3333    0.5516 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.6944    0.3506    1.3281 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.7470   -0.5047    0.6756 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.0536   -0.0326   -0.7246 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0311    1.5744    1.4804 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.4521   -0.0777    1.9883 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.6008    1.3419    2.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.1927    1.5402    0.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.7117    0.8841   -0.5485 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.2022   -0.3511    0.7697 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.8172   -0.6104   -0.9237 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.7264   -2.5707    0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.5365   -1.8782    1.5601 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.5575   -3.5480    0.2797 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.0054   -2.9306   -1.3020 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.0800   -1.7078    0.7943 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.4848   -0.8840   -0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2115   -3.6073   -0.3534 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5601   -2.9326   -1.9719 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1823   -0.9293   -1.5474 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2675   -2.4768   -1.3309 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3257   -0.8472    1.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2075   -2.3278    1.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1204   -0.1590    1.3392 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8273    0.3924   -0.2142 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0013   -2.0938    0.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5527   -1.5048   -1.4017 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7528    0.0858    0.5331 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3119   -0.8877   -0.9112 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4123    1.3792   -0.7787 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0070    0.5499   -2.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5735    2.6454   -0.5639 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2534    2.7976   -2.1716 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9336    2.9933   -2.3914 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2635    1.4458   -3.1498 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5025    0.2748   -0.9402 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2220    1.9567   -0.3226 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1411    0.6978   -2.8953 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7944    2.3503   -2.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0897   -0.2124   -0.8098 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8823    0.6506   -1.7869 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4532    1.5256    0.7029 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6863    1.3223    0.6089 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3169    3.4827   -0.7411 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1966    3.7139    0.5938 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2784    2.9426   -2.2432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1631    4.4818   -1.3783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0780    1.9631   -0.3167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3285    3.6905    0.2928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2100    4.3403   -1.9060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1579    2.5932   -2.4438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    3.8057   -0.0769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4342    3.3422   -1.6328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8645    2.2441    0.1605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6440   -0.4349    0.7234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0301    0.5994    2.8194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6926    1.0770    2.4692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7670   -0.8163    3.6050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7566   -1.5395    0.3168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2955   -0.1366   -1.5847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1683    0.9099   -1.4651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2343   -0.5205   -1.3638 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.1464    1.6521   -0.7539 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0011770 (Cer(d18:0/25:0))


  Mrv0541 02241201542D          

 47 46  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0011770

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C43H87NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-27-29-31-33-35-37-39-43(47)44-41(40-45)42(46)38-36-34-32-30-28-26-16-14-12-10-8-6-4-2/h41-42,45-46H,3-40H2,1-2H3,(H,44,47)/t41-,42+/m0/s1

> <INCHI_KEY>
HCDLRJUFVJOBJP-ACEXITHZSA-N

> <FORMULA>
C43H87NO3

> <MOLECULAR_WEIGHT>
666.1558

> <EXACT_MASS>
665.668595655

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
93.00395389659184

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]pentacosanamide

> <ALOGPS_LOGP>
10.31

> <JCHEM_LOGP>
15.072487325333336

> <ALOGPS_LOGS>
-7.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.492196702047824

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.831978572939391

> <JCHEM_PKA_STRONGEST_BASIC>
0.033682907246806226

> <JCHEM_POLAR_SURFACE_AREA>
69.56

> <JCHEM_REFRACTIVITY>
206.2221

> <JCHEM_ROTATABLE_BOND_COUNT>
40

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.04e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]pentacosanamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0011770 (Cer(d18:0/25:0))

HMDB0011770
     RDKit          3D
Cer(d18:0/25:0)
134133  0  0  0  0  0  0  0  0999 V2000
   15.8838    0.8740    1.5817 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4474    0.6484    0.1935 C   0  0  0  0  0  0  0  0  0  0  0  0
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   15.0311    1.5744    1.4804 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.4521   -0.0777    1.9883 H   0  0  0  0  0  0  0  0  0  0  0  0
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   17.1927    1.5402    0.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.7117    0.8841   -0.5485 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.2022   -0.3511    0.7697 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.8172   -0.6104   -0.9237 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.7264   -2.5707    0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.5365   -1.8782    1.5601 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.5575   -3.5480    0.2797 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.0054   -2.9306   -1.3020 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.0800   -1.7078    0.7943 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.4848   -0.8840   -0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2115   -3.6073   -0.3534 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5601   -2.9326   -1.9719 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1823   -0.9293   -1.5474 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2675   -2.4768   -1.3309 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3257   -0.8472    1.0743 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2075   -2.3278    1.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1204   -0.1590    1.3392 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8273    0.3924   -0.2142 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.3119   -0.8877   -0.9112 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4123    1.3792   -0.7787 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0070    0.5499   -2.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5735    2.6454   -0.5639 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2534    2.7976   -2.1716 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9336    2.9933   -2.3914 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2635    1.4458   -3.1498 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5025    0.2748   -0.9402 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2220    1.9567   -0.3226 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1411    0.6978   -2.8953 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7944    2.3503   -2.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0897   -0.2124   -0.8098 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8823    0.6506   -1.7869 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4532    1.5256    0.7029 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6863    1.3223    0.6089 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.6440   -0.4349    0.7234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0301    0.5994    2.8194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6926    1.0770    2.4692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7670   -0.8163    3.6050 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.2955   -0.1366   -1.5847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1683    0.9099   -1.4651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2343   -0.5205   -1.3638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0933    1.7757    0.7208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1464    1.6521   -0.7539 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.8416    0.0397    2.7898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5794   -0.1925    2.7841 H   0  0  0  0  0  0  0  0  0  0  0  0
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  -18.1587    0.0659   -0.8141 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0011770 (Cer(d18:0/25:0))

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      38.860  -6.219   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      37.518  -5.464   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      36.193  -6.248   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      34.850  -5.493   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      33.525  -6.278   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      32.183  -5.523   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      30.858  -6.308   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      29.516  -5.553   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      28.191  -6.338   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.849  -5.583   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      25.524  -6.368   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.181  -5.613   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      22.856  -6.398   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      21.514  -5.643   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      20.189  -6.427   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      18.847  -5.672   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      17.522  -6.457   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      16.180  -5.702   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      34.833  -3.953   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      36.210  -7.788   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      14.854  -6.487   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.201  -7.788   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.535  -8.558   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.869  -7.788   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       8.203  -8.558   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.536  -7.788   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.870  -8.558   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.204  -7.788   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.537  -8.558   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      14.871  -7.788   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      16.205  -8.558   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      17.538  -7.788   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      18.872  -8.558   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      20.206  -7.788   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      21.539  -8.558   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      22.873  -7.788   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      24.207  -8.558   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      25.540  -7.788   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      26.874  -8.558   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      28.208  -7.788   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      29.541  -8.558   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      30.875  -7.788   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      32.209  -8.558   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      33.543  -7.788   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      34.876  -8.558   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      34.876 -10.098   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0       2.868  -8.558   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   21                                                       
CONECT   19    4                                                            
CONECT   20    3   45                                                       
CONECT   21   18                                                            
CONECT   22   23   47                                                       
CONECT   23   22   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   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   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   20   46                                                  
CONECT   46   45                                                            
CONECT   47   22                                                            
MASTER        0    0    0    0    0    0    0    0   47    0   92    0
END
Download

3D PDB for HMDB0011770 (Cer(d18:0/25:0))

COMPND    HMDB0011770
HETATM    1  C1  UNL     1      15.884   0.874   1.582  1.00  0.00           C  
HETATM    2  C2  UNL     1      16.447   0.648   0.193  1.00  0.00           C  
HETATM    3  C3  UNL     1      17.301  -0.546   0.088  1.00  0.00           C  
HETATM    4  C4  UNL     1      16.807  -1.876   0.426  1.00  0.00           C  
HETATM    5  C5  UNL     1      15.727  -2.561  -0.276  1.00  0.00           C  
HETATM    6  C6  UNL     1      14.427  -1.860  -0.252  1.00  0.00           C  
HETATM    7  C7  UNL     1      13.319  -2.675  -0.936  1.00  0.00           C  
HETATM    8  C8  UNL     1      12.072  -1.812  -0.896  1.00  0.00           C  
HETATM    9  C9  UNL     1      11.624  -1.437   0.472  1.00  0.00           C  
HETATM   10  C10 UNL     1      10.404  -0.500   0.321  1.00  0.00           C  
HETATM   11  C11 UNL     1       9.300  -1.196  -0.352  1.00  0.00           C  
HETATM   12  C12 UNL     1       8.093  -0.220  -0.459  1.00  0.00           C  
HETATM   13  C13 UNL     1       8.487   0.909  -1.303  1.00  0.00           C  
HETATM   14  C14 UNL     1       7.619   2.054  -1.563  1.00  0.00           C  
HETATM   15  C15 UNL     1       6.283   1.935  -2.137  1.00  0.00           C  
HETATM   16  C16 UNL     1       5.274   1.304  -1.218  1.00  0.00           C  
HETATM   17  C17 UNL     1       3.963   1.313  -1.989  1.00  0.00           C  
HETATM   18  C18 UNL     1       2.792   0.791  -1.180  1.00  0.00           C  
HETATM   19  C19 UNL     1       2.576   1.657   0.052  1.00  0.00           C  
HETATM   20  C20 UNL     1       2.355   3.097  -0.346  1.00  0.00           C  
HETATM   21  C21 UNL     1       1.208   3.360  -1.227  1.00  0.00           C  
HETATM   22  C22 UNL     1      -0.146   3.028  -0.590  1.00  0.00           C  
HETATM   23  C23 UNL     1      -1.259   3.280  -1.549  1.00  0.00           C  
HETATM   24  C24 UNL     1      -2.585   3.060  -0.924  1.00  0.00           C  
HETATM   25  C25 UNL     1      -2.879   1.734  -0.379  1.00  0.00           C  
HETATM   26  O1  UNL     1      -2.046   0.826  -0.379  1.00  0.00           O  
HETATM   27  N1  UNL     1      -4.179   1.457   0.184  1.00  0.00           N  
HETATM   28  C26 UNL     1      -4.596   0.222   0.761  1.00  0.00           C  
HETATM   29  C27 UNL     1      -4.940   0.287   2.214  1.00  0.00           C  
HETATM   30  O2  UNL     1      -5.302  -0.947   2.738  1.00  0.00           O  
HETATM   31  C28 UNL     1      -5.567  -0.573  -0.098  1.00  0.00           C  
HETATM   32  O3  UNL     1      -4.770  -0.939  -1.299  1.00  0.00           O  
HETATM   33  C29 UNL     1      -6.661   0.217  -0.671  1.00  0.00           C  
HETATM   34  C30 UNL     1      -7.638   0.936   0.083  1.00  0.00           C  
HETATM   35  C31 UNL     1      -8.737   0.521   0.924  1.00  0.00           C  
HETATM   36  C32 UNL     1      -8.672  -0.345   2.098  1.00  0.00           C  
HETATM   37  C33 UNL     1      -8.393  -1.793   1.926  1.00  0.00           C  
HETATM   38  C34 UNL     1      -9.474  -2.487   1.092  1.00  0.00           C  
HETATM   39  C35 UNL     1     -10.818  -2.394   1.784  1.00  0.00           C  
HETATM   40  C36 UNL     1     -11.861  -3.098   0.966  1.00  0.00           C  
HETATM   41  C37 UNL     1     -12.089  -2.521  -0.399  1.00  0.00           C  
HETATM   42  C38 UNL     1     -12.563  -1.104  -0.301  1.00  0.00           C  
HETATM   43  C39 UNL     1     -13.885  -1.084   0.470  1.00  0.00           C  
HETATM   44  C40 UNL     1     -14.410   0.333   0.552  1.00  0.00           C  
HETATM   45  C41 UNL     1     -15.694   0.351   1.328  1.00  0.00           C  
HETATM   46  C42 UNL     1     -16.747  -0.505   0.676  1.00  0.00           C  
HETATM   47  C43 UNL     1     -17.054  -0.033  -0.725  1.00  0.00           C  
HETATM   48  H1  UNL     1      15.031   1.574   1.480  1.00  0.00           H  
HETATM   49  H2  UNL     1      15.452  -0.078   1.988  1.00  0.00           H  
HETATM   50  H3  UNL     1      16.601   1.342   2.264  1.00  0.00           H  
HETATM   51  H4  UNL     1      17.193   1.540   0.089  1.00  0.00           H  
HETATM   52  H5  UNL     1      15.712   0.884  -0.548  1.00  0.00           H  
HETATM   53  H6  UNL     1      18.202  -0.351   0.770  1.00  0.00           H  
HETATM   54  H7  UNL     1      17.817  -0.610  -0.924  1.00  0.00           H  
HETATM   55  H8  UNL     1      17.726  -2.571   0.476  1.00  0.00           H  
HETATM   56  H9  UNL     1      16.536  -1.878   1.560  1.00  0.00           H  
HETATM   57  H10 UNL     1      15.558  -3.548   0.280  1.00  0.00           H  
HETATM   58  H11 UNL     1      16.005  -2.931  -1.302  1.00  0.00           H  
HETATM   59  H12 UNL     1      14.080  -1.708   0.794  1.00  0.00           H  
HETATM   60  H13 UNL     1      14.485  -0.884  -0.734  1.00  0.00           H  
HETATM   61  H14 UNL     1      13.212  -3.607  -0.353  1.00  0.00           H  
HETATM   62  H15 UNL     1      13.560  -2.933  -1.972  1.00  0.00           H  
HETATM   63  H16 UNL     1      12.182  -0.929  -1.547  1.00  0.00           H  
HETATM   64  H17 UNL     1      11.268  -2.477  -1.331  1.00  0.00           H  
HETATM   65  H18 UNL     1      12.326  -0.847   1.074  1.00  0.00           H  
HETATM   66  H19 UNL     1      11.208  -2.328   1.026  1.00  0.00           H  
HETATM   67  H20 UNL     1      10.120  -0.159   1.339  1.00  0.00           H  
HETATM   68  H21 UNL     1      10.827   0.392  -0.214  1.00  0.00           H  
HETATM   69  H22 UNL     1       9.001  -2.094   0.188  1.00  0.00           H  
HETATM   70  H23 UNL     1       9.553  -1.505  -1.402  1.00  0.00           H  
HETATM   71  H24 UNL     1       7.753   0.086   0.533  1.00  0.00           H  
HETATM   72  H25 UNL     1       7.312  -0.888  -0.911  1.00  0.00           H  
HETATM   73  H26 UNL     1       9.412   1.379  -0.779  1.00  0.00           H  
HETATM   74  H27 UNL     1       9.007   0.550  -2.270  1.00  0.00           H  
HETATM   75  H28 UNL     1       7.573   2.645  -0.564  1.00  0.00           H  
HETATM   76  H29 UNL     1       8.253   2.798  -2.172  1.00  0.00           H  
HETATM   77  H30 UNL     1       5.934   2.993  -2.391  1.00  0.00           H  
HETATM   78  H31 UNL     1       6.263   1.446  -3.150  1.00  0.00           H  
HETATM   79  H32 UNL     1       5.503   0.275  -0.940  1.00  0.00           H  
HETATM   80  H33 UNL     1       5.222   1.957  -0.323  1.00  0.00           H  
HETATM   81  H34 UNL     1       4.141   0.698  -2.895  1.00  0.00           H  
HETATM   82  H35 UNL     1       3.794   2.350  -2.351  1.00  0.00           H  
HETATM   83  H36 UNL     1       3.090  -0.212  -0.810  1.00  0.00           H  
HETATM   84  H37 UNL     1       1.882   0.651  -1.787  1.00  0.00           H  
HETATM   85  H38 UNL     1       3.453   1.526   0.703  1.00  0.00           H  
HETATM   86  H39 UNL     1       1.686   1.322   0.609  1.00  0.00           H  
HETATM   87  H40 UNL     1       3.317   3.483  -0.741  1.00  0.00           H  
HETATM   88  H41 UNL     1       2.197   3.714   0.594  1.00  0.00           H  
HETATM   89  H42 UNL     1       1.278   2.943  -2.243  1.00  0.00           H  
HETATM   90  H43 UNL     1       1.163   4.482  -1.378  1.00  0.00           H  
HETATM   91  H44 UNL     1      -0.078   1.963  -0.317  1.00  0.00           H  
HETATM   92  H45 UNL     1      -0.329   3.690   0.293  1.00  0.00           H  
HETATM   93  H46 UNL     1      -1.210   4.340  -1.906  1.00  0.00           H  
HETATM   94  H47 UNL     1      -1.158   2.593  -2.444  1.00  0.00           H  
HETATM   95  H48 UNL     1      -2.751   3.806  -0.077  1.00  0.00           H  
HETATM   96  H49 UNL     1      -3.434   3.342  -1.633  1.00  0.00           H  
HETATM   97  H50 UNL     1      -4.864   2.244   0.161  1.00  0.00           H  
HETATM   98  H51 UNL     1      -3.644  -0.435   0.723  1.00  0.00           H  
HETATM   99  H52 UNL     1      -4.030   0.599   2.819  1.00  0.00           H  
HETATM  100  H53 UNL     1      -5.693   1.077   2.469  1.00  0.00           H  
HETATM  101  H54 UNL     1      -5.767  -0.816   3.605  1.00  0.00           H  
HETATM  102  H55 UNL     1      -5.757  -1.540   0.317  1.00  0.00           H  
HETATM  103  H56 UNL     1      -4.295  -0.137  -1.585  1.00  0.00           H  
HETATM  104  H57 UNL     1      -6.168   0.910  -1.465  1.00  0.00           H  
HETATM  105  H58 UNL     1      -7.234  -0.520  -1.364  1.00  0.00           H  
HETATM  106  H59 UNL     1      -7.093   1.776   0.721  1.00  0.00           H  
HETATM  107  H60 UNL     1      -8.146   1.652  -0.754  1.00  0.00           H  
HETATM  108  H61 UNL     1      -9.303   1.505   1.235  1.00  0.00           H  
HETATM  109  H62 UNL     1      -9.543   0.108   0.186  1.00  0.00           H  
HETATM  110  H63 UNL     1      -7.842   0.040   2.790  1.00  0.00           H  
HETATM  111  H64 UNL     1      -9.579  -0.193   2.784  1.00  0.00           H  
HETATM  112  H65 UNL     1      -8.470  -2.267   2.951  1.00  0.00           H  
HETATM  113  H66 UNL     1      -7.429  -1.993   1.508  1.00  0.00           H  
HETATM  114  H67 UNL     1      -9.518  -2.074   0.073  1.00  0.00           H  
HETATM  115  H68 UNL     1      -9.194  -3.552   1.024  1.00  0.00           H  
HETATM  116  H69 UNL     1     -10.710  -2.964   2.735  1.00  0.00           H  
HETATM  117  H70 UNL     1     -11.147  -1.377   1.993  1.00  0.00           H  
HETATM  118  H71 UNL     1     -11.523  -4.174   0.760  1.00  0.00           H  
HETATM  119  H72 UNL     1     -12.827  -3.203   1.499  1.00  0.00           H  
HETATM  120  H73 UNL     1     -12.865  -3.174  -0.887  1.00  0.00           H  
HETATM  121  H74 UNL     1     -11.176  -2.607  -1.042  1.00  0.00           H  
HETATM  122  H75 UNL     1     -12.694  -0.651  -1.309  1.00  0.00           H  
HETATM  123  H76 UNL     1     -11.829  -0.497   0.245  1.00  0.00           H  
HETATM  124  H77 UNL     1     -14.566  -1.791  -0.016  1.00  0.00           H  
HETATM  125  H78 UNL     1     -13.686  -1.442   1.498  1.00  0.00           H  
HETATM  126  H79 UNL     1     -14.557   0.694  -0.496  1.00  0.00           H  
HETATM  127  H80 UNL     1     -13.654   0.985   1.031  1.00  0.00           H  
HETATM  128  H81 UNL     1     -16.066   1.380   1.521  1.00  0.00           H  
HETATM  129  H82 UNL     1     -15.496  -0.096   2.338  1.00  0.00           H  
HETATM  130  H83 UNL     1     -16.415  -1.553   0.685  1.00  0.00           H  
HETATM  131  H84 UNL     1     -17.669  -0.410   1.323  1.00  0.00           H  
HETATM  132  H85 UNL     1     -16.746  -0.825  -1.462  1.00  0.00           H  
HETATM  133  H86 UNL     1     -16.570   0.934  -0.936  1.00  0.00           H  
HETATM  134  H87 UNL     1     -18.159   0.066  -0.814  1.00  0.00           H  
CONECT    1    2   48   49   50
CONECT    2    3   51   52
CONECT    3    4   53   54
CONECT    4    5   55   56
CONECT    5    6   57   58
CONECT    6    7   59   60
CONECT    7    8   61   62
CONECT    8    9   63   64
CONECT    9   10   65   66
CONECT   10   11   67   68
CONECT   11   12   69   70
CONECT   12   13   71   72
CONECT   13   14   73   74
CONECT   14   15   75   76
CONECT   15   16   77   78
CONECT   16   17   79   80
CONECT   17   18   81   82
CONECT   18   19   83   84
CONECT   19   20   85   86
CONECT   20   21   87   88
CONECT   21   22   89   90
CONECT   22   23   91   92
CONECT   23   24   93   94
CONECT   24   25   95   96
CONECT   25   26   26   27
CONECT   27   28   97
CONECT   28   29   31   98
CONECT   29   30   99  100
CONECT   30  101
CONECT   31   32   33  102
CONECT   32  103
CONECT   33   34  104  105
CONECT   34   35  106  107
CONECT   35   36  108  109
CONECT   36   37  110  111
CONECT   37   38  112  113
CONECT   38   39  114  115
CONECT   39   40  116  117
CONECT   40   41  118  119
CONECT   41   42  120  121
CONECT   42   43  122  123
CONECT   43   44  124  125
CONECT   44   45  126  127
CONECT   45   46  128  129
CONECT   46   47  130  131
CONECT   47  132  133  134
END
Download

SMILES for HMDB0011770 (Cer(d18:0/25:0))

CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC
Download

INCHI for HMDB0011770 (Cer(d18:0/25:0))

InChI=1S/C43H87NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-27-29-31-33-35-37-39-43(47)44-41(40-45)42(46)38-36-34-32-30-28-26-16-14-12-10-8-6-4-2/h41-42,45-46H,3-40H2,1-2H3,(H,44,47)/t41-,42+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
CeramideHMDB
N-(Pentacosanoyl)-sphinganineHMDB
Ceramide(D18:0/25:0)HMDB
N-(Pentacosanoyl)-dihydrosphingosineHMDB
N-(Pentacosanoyl)-D-erythro-sphinganineHMDB
N-[(2S,3R)-1,3-Dihydroxyoctadecan-2-yl]pentacosanimidateHMDB
Chemical FormulaC43H87NO3
Average Molecular Weight666.1558
Monoisotopic Molecular Weight665.668595655
IUPAC NameN-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]pentacosanamide
Traditional NameN-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]pentacosanamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C43H87NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-27-29-31-33-35-37-39-43(47)44-41(40-45)42(46)38-36-34-32-30-28-26-16-14-12-10-8-6-4-2/h41-42,45-46H,3-40H2,1-2H3,(H,44,47)/t41-,42+/m0/s1
InChI KeyHCDLRJUFVJOBJP-ACEXITHZSA-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 DescriptorsNot Available
Ontology
Physiological effect
Health effectOrganoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility2.0e-05 g/LALOGPS
logP10.31ALOGPS
logP15.07ChemAxon
logS-7.5ALOGPS
pKa (Strongest Acidic)13.83ChemAxon
pKa (Strongest Basic)0.034ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count40ChemAxon
Refractivity206.22 m³·mol⁻¹ChemAxon
Polarizability93 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]+275.79631661259
DarkChem[M-H]-267.39731661259
DeepCCS[M+H]+269.27430932474
DeepCCS[M-H]-266.91630932474
DeepCCS[M-2H]-299.79930932474
DeepCCS[M+Na]+276.06830932474
AllCCS[M+H]+288.032859911
AllCCS[M+H-H2O]+287.732859911
AllCCS[M+NH4]+288.432859911
AllCCS[M+Na]+288.432859911
AllCCS[M-H]-279.032859911
AllCCS[M+Na-2H]-282.032859911
AllCCS[M+HCOO]-285.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Cer(d18:0/25:0)CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC3825.5Standard polar33892256
Cer(d18:0/25:0)CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC4161.9Standard non polar33892256
Cer(d18:0/25:0)CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC5187.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Cer(d18:0/25:0),3TMS,isomer #1CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@@H](CCCCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C5030.6Semi standard non polar33892256
Cer(d18:0/25:0),3TMS,isomer #1CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@@H](CCCCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4669.0Standard non polar33892256
Cer(d18:0/25:0),3TMS,isomer #1CCCCCCCCCCCCCCCCCCCCCCCCC(=O)N([C@@H](CO[Si](C)(C)C)[C@@H](CCCCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4812.1Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cer(d18:0/25:0) GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 10V, Positive-QTOFsplash10-014i-0000009000-c463b84b012f25bb561e2017-10-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 20V, Positive-QTOFsplash10-014i-0050009000-a4566ef141d2e2bf62172017-10-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 40V, Positive-QTOFsplash10-015a-0090005000-edcfb50b3f3431d5afa92017-10-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 10V, Positive-QTOFsplash10-014i-0000009000-844019b6c99c174a8f5c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 20V, Positive-QTOFsplash10-014i-0050009000-5c568dec55607f49029f2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 40V, Positive-QTOFsplash10-015a-0090005000-f51f771380a467b5db8f2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 10V, Positive-QTOFsplash10-00di-0000009000-200f9fd0912ab13704f52021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 20V, Positive-QTOFsplash10-00di-0000009000-200f9fd0912ab13704f52021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 40V, Positive-QTOFsplash10-0udi-0000009000-edcb0d02f6579b7699d72021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 10V, Negative-QTOFsplash10-03di-0000009000-7e9f9ded5db43c36856b2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 20V, Negative-QTOFsplash10-03di-0010009000-6043e61861415b5fa6ae2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d18:0/25:0) 40V, Negative-QTOFsplash10-01q9-0022009000-0dcf67ab5b3b515297352021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedNewborn (0-30 days old)Not Specified
Premature neonates		 details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028440
KNApSAcK IDNot Available
Chemspider ID24765765
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481050
PDB IDNot Available
ChEBI IDNot Available
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. Bowser PA, Gray GM: Sphingomyelinase in pig and human epidermis. J Invest Dermatol. 1978 Jun;70(6):331-5. [PubMed:25935 ]
  2. 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 ]
  3. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  4. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  5. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  6. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  7. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  8. Ghosh S, Strum JC, Bell RM: Lipid biochemistry: functions of glycerolipids and sphingolipids in cellular signaling. FASEB J. 1997 Jan;11(1):45-50. [PubMed:9034165 ]
  9. Pruett ST, Bushnev A, Hagedorn K, Adiga M, Haynes CA, Sullards MC, Liotta DC, Merrill AH Jr: Biodiversity of sphingoid bases ("sphingosines") and related amino alcohols. J Lipid Res. 2008 Aug;49(8):1621-39. doi: 10.1194/jlr.R800012-JLR200. Epub 2008 May 21. [PubMed:18499644 ]
  10. Hannun YA, Obeid LM: Ceramide: an intracellular signal for apoptosis. Trends Biochem Sci. 1995 Feb;20(2):73-7. [PubMed:7701566 ]
  11. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  12. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Only showing the first 10 proteins. There are 66 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. 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
2. 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
3. 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
4. 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
5. 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
6. 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
Enzyme Details
7. Ceramide glucosyltransferase
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Catalyzes the first glycosylation step in glycosphingolipid biosynthesis, the transfer of glucose to ceramide. May also serve as a "flippase".
Gene Name:
UGCG
Uniprot ID:
Q16739
Molecular weight:
44853.255
Enzyme Details
8. Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGQ
Uniprot ID:
Q9BRB3
Molecular weight:
65343.25
Enzyme Details
9. Phosphatidylinositol N-acetylglucosaminyltransferase subunit A
General function:
Involved in biosynthetic process
Specific function:
Necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, the very early intermediate in GPI-anchor biosynthesis.
Gene Name:
PIGA
Uniprot ID:
P37287
Molecular weight:
54126.065
Enzyme Details
10. Phosphatidylinositol N-acetylglucosaminyltransferase subunit H
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGH
Uniprot ID:
Q14442
Molecular weight:
21080.415

Only showing the first 10 proteins. There are 66 proteins in total.

Show all enzymes and transporters