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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2020-06-11 22:31:44 UTC

Update Date

2022-11-30 19:53:43 UTC

HMDB ID

HMDB0240684

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Cer(d20:1/18:0)

Description

Cer(d20:1/18:0), also known as N-octadecanoyl-eicosasphing-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(d20:1/18:0) is a colorless solid that consists of an unsaturated 20-carbon sphingoid base with an attached saturated octadecanoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Cer(d20:1/18:0)
  Mrv1652306122000302D          

 43 42  0  0  0  0            999 V2000
   -2.3824    0.3590    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6679    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9699   -0.3554    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7950   -0.3554    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9590    0.3595    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0969    0.7716    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0969    1.5430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8110    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5251    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2392    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9534    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6675    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3816    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0957    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8099    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.5240    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2381    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9522    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6664    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3805    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.0946    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.8087    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.5228    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2370    0.3585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5095   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5095   -1.5393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2236   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9377   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6518   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3660   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0801   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7942   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5083   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2225   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9366   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6507   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3648   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0790   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7931   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.5072   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.2213   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.9355   -0.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.6496   -0.3548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  1  3  1  1  0  0  0
  1  4  1  6  0  0  0
  5  2  1  0  0  0  0
  4 25  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 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
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
M  END

HMDB0240684
     RDKit          3D
Cer(d20:1/18:0)
117116  0  0  0  0  0  0  0  0999 V2000
   14.6186   -1.7931    1.3776 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9723   -0.5525    0.8223 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8370   -0.1122    1.7236 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7805   -1.1726    1.8451 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1616   -1.5360    0.5326 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5138   -0.3349   -0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4355    0.1848    0.8135 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7330    1.3974    0.2395 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0800    1.1148   -1.0684 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0426    0.0445   -1.0358 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8869    0.2980   -0.1256 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1280    1.5576   -0.4809 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5720    1.5454   -1.8404 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6382    0.5234   -2.3105 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3347    0.4181   -1.6336 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4051   -0.0127   -0.2278 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7920   -1.1590    0.1459 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8490   -1.6040    1.5351 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9927   -1.2394    2.2054 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5942   -1.0627    2.2173 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5254   -1.6428    3.6172 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6483   -1.3333    4.3759 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5892   -1.4198    1.5051 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290   -0.3738    0.9999 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0959    0.8131    1.2075 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6446   -0.7077    0.2593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3768    0.4767   -0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5302    1.1672   -1.3404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0477    2.3666   -2.0160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2219    2.3313   -2.8835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5406    1.9034   -2.3587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0335    2.6898   -1.1976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4099    2.1588   -0.6880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3982    2.2997   -1.7633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8046    1.9863   -1.5053 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2689    0.6539   -1.1108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8474    0.1610    0.2228 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4361   -1.2451    0.4054 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9186   -1.1932    0.3493 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4357   -2.6278    0.5558 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.9565   -2.5256    0.4896 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3761   -1.5929    1.6010 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6687   -1.6729    2.4780 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.1286   -2.7314    1.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6600   -1.8359    0.9759 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.7370    0.2493    0.8097 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6186   -0.7107   -0.2278 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4237    0.8359    1.3752 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2889    0.0075    2.7436 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0559   -0.8594    2.6178 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2923   -2.0805    2.2977 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3479   -2.3000    0.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.9001   -1.9454   -0.1728 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2930    0.4363   -0.2589 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0470   -0.6544   -1.0603 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6980   -0.5960    1.0520 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8735    0.5125    1.7810 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9836    1.7409    0.9664 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5262    2.1605    0.0673 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8596    0.7974   -1.7997 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7003    2.0805   -1.4716 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6821   -0.1197   -2.0733 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5408   -0.8910   -0.6854 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1982   -0.5534   -0.1976 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2239    0.3845    0.9310 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5272    1.8765    0.3535 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9348    2.4167   -0.5145 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1270    2.6039   -1.9945 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4541    1.5278   -2.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4448    0.6226   -3.4323 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1131   -0.5278   -2.2214 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6237   -0.2531   -2.2054 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7722    1.4007   -1.6301 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8909    0.5008    0.5679 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2728   -1.7152   -0.6061 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7278   -2.7341    1.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3730   -2.0246    2.6364 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7014    0.0364    2.2368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4034   -1.3550    4.1305 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5165   -2.7557    3.5199 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7203   -0.3483    4.3878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8500   -2.4145    1.3486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3161   -1.2742    0.9617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4413   -1.4579   -0.5569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5669    1.1953    0.4988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3090    0.0680   -0.7441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5689    1.4856   -0.8310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1239    0.4019   -2.0986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0965    3.1886   -1.2364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1813    2.7436   -2.6699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3255    3.3210   -3.4483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9927    1.6164   -3.7494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2764    2.2145   -3.2183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6653    0.8323   -2.3419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3503    2.5604   -0.3421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2573    3.7482   -1.4430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6686    2.7561    0.1927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2069    1.1046   -0.3661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0628    1.7278   -2.7022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3615    3.3803   -2.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4030    2.3427   -2.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1406    2.7700   -0.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0613   -0.1200   -1.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4179    0.7012   -1.1664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8094    0.1767    0.4919 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3686    0.7517    1.0524 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1353   -1.6019    1.4035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9852   -1.8642   -0.4134 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3539   -0.8948   -0.6276 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2892   -0.5122    1.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0947   -2.9489    1.5602 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0448   -3.2530   -0.2652 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.4209   -3.5135    0.5336 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.1712   -2.0145   -0.4954 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

Cer(d20:1/18:0)
  Mrv1652306122000302D          

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  1  6  1  0  0  0  0
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  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
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 42 43  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0240684

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](CO)(NC(=O)CCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C38H75NO3/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-37(41)36(35-40)39-38(42)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h31,33,36-37,40-41H,3-30,32,34-35H2,1-2H3,(H,39,42)/b33-31+/t36-,37+/m0/s1

> <INCHI_KEY>
BDIIZHQNVIYLPJ-NUKVNZTCSA-N

> <FORMULA>
C38H75NO3

> <MOLECULAR_WEIGHT>
594.022

> <EXACT_MASS>
593.574695279

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
117

> <JCHEM_AVERAGE_POLARIZABILITY>
81.6292388350414

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2S,3R,4E)-1,3-dihydroxyicos-4-en-2-yl]octadecanamide

> <ALOGPS_LOGP>
10.01

> <JCHEM_LOGP>
12.643629803666666

> <ALOGPS_LOGS>
-7.37

> <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>
184.1797

> <JCHEM_ROTATABLE_BOND_COUNT>
34

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.55e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2S,3R,4E)-1,3-dihydroxyicos-4-en-2-yl]octadecanamide

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0240684
     RDKit          3D
Cer(d20:1/18:0)
117116  0  0  0  0  0  0  0  0999 V2000
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   -0.8500   -2.4145    1.3486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3161   -1.2742    0.9617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4413   -1.4579   -0.5569 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5669    1.1953    0.4988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3090    0.0680   -0.7441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5689    1.4856   -0.8310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1239    0.4019   -2.0986 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0965    3.1886   -1.2364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1813    2.7436   -2.6699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3255    3.3210   -3.4483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9927    1.6164   -3.7494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2764    2.2145   -3.2183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6653    0.8323   -2.3419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3503    2.5604   -0.3421 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2573    3.7482   -1.4430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6686    2.7561    0.1927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2069    1.1046   -0.3661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0628    1.7278   -2.7022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3615    3.3803   -2.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4030    2.3427   -2.4342 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1406    2.7700   -0.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0613   -0.1200   -1.9152 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4179    0.7012   -1.1664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8094    0.1767    0.4919 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3686    0.7517    1.0524 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1353   -1.6019    1.4035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9852   -1.8642   -0.4134 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3539   -0.8948   -0.6276 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2892   -0.5122    1.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0947   -2.9489    1.5602 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0448   -3.2530   -0.2652 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.4209   -3.5135    0.5336 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.1712   -2.0145   -0.4954 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.3895   -1.8622    1.9472 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6652   -1.6599    2.4649 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3525   -0.5349    1.2599 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 21 22  1  0
 20 23  1  0
 23 24  1  0
 24 25  2  0
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 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
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 34 35  1  0
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 37 38  1  0
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 39 40  1  0
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  1 43  1  0
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 11 64  1  0
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 42117  1  0
M  END

HEADER    PROTEIN                                 12-JUN-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Cer(d20:1/18:0)                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-JUN-20         0                                  
HETATM    1  C   UNK     0      -4.447   0.670   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.113   1.440   0.000  0.00  0.00           C+0
HETATM    3  H   UNK     0      -3.677  -0.663   0.000  0.00  0.00           H+0
HETATM    4  N   UNK     0      -5.217  -0.663   0.000  0.00  0.00           N+0
HETATM    5  O   UNK     0      -1.790   0.671   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -5.781   1.440   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.781   2.880   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -7.114   0.669   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -8.447   1.440   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -9.780   0.669   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0     -11.113   1.440   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -12.446   0.669   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0     -13.779   1.440   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0     -15.112   0.669   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -16.445   1.440   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0     -17.778   0.669   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -19.111   1.440   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0     -20.444   0.669   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -21.777   1.440   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0     -23.110   0.669   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0     -24.443   1.440   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -25.776   0.669   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -27.109   1.440   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -28.442   0.669   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -6.551  -1.433   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -6.551  -2.873   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -7.884  -0.662   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -9.217  -1.433   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0     -10.550  -0.662   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0     -11.883  -1.433   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0     -13.216  -0.662   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -14.549  -1.433   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -15.882  -0.662   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -17.215  -1.433   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -18.548  -0.662   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -19.881  -1.433   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -21.214  -0.662   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -22.547  -1.433   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -23.880  -0.662   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -25.213  -1.433   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -26.546  -0.662   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -27.880  -1.433   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -29.213  -0.662   0.000  0.00  0.00           C+0
CONECT    1    2    3    4    6                                             
CONECT    2    1    5                                                       
CONECT    3    1                                                            
CONECT    4    1   25                                                       
CONECT    5    2                                                            
CONECT    6    1    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    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   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25    4   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   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                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   84    0
END

COMPND    HMDB0240684
HETATM    1  C1  UNL     1      14.619  -1.793   1.378  1.00  0.00           C  
HETATM    2  C2  UNL     1      13.972  -0.552   0.822  1.00  0.00           C  
HETATM    3  C3  UNL     1      12.837  -0.112   1.724  1.00  0.00           C  
HETATM    4  C4  UNL     1      11.781  -1.173   1.845  1.00  0.00           C  
HETATM    5  C5  UNL     1      11.162  -1.536   0.533  1.00  0.00           C  
HETATM    6  C6  UNL     1      10.514  -0.335  -0.101  1.00  0.00           C  
HETATM    7  C7  UNL     1       9.435   0.185   0.814  1.00  0.00           C  
HETATM    8  C8  UNL     1       8.733   1.397   0.240  1.00  0.00           C  
HETATM    9  C9  UNL     1       8.080   1.115  -1.068  1.00  0.00           C  
HETATM   10  C10 UNL     1       7.043   0.044  -1.036  1.00  0.00           C  
HETATM   11  C11 UNL     1       5.887   0.298  -0.126  1.00  0.00           C  
HETATM   12  C12 UNL     1       5.128   1.558  -0.481  1.00  0.00           C  
HETATM   13  C13 UNL     1       4.572   1.545  -1.840  1.00  0.00           C  
HETATM   14  C14 UNL     1       3.638   0.523  -2.310  1.00  0.00           C  
HETATM   15  C15 UNL     1       2.335   0.418  -1.634  1.00  0.00           C  
HETATM   16  C16 UNL     1       2.405  -0.013  -0.228  1.00  0.00           C  
HETATM   17  C17 UNL     1       1.792  -1.159   0.146  1.00  0.00           C  
HETATM   18  C18 UNL     1       1.849  -1.604   1.535  1.00  0.00           C  
HETATM   19  O1  UNL     1       2.993  -1.239   2.205  1.00  0.00           O  
HETATM   20  C19 UNL     1       0.594  -1.063   2.217  1.00  0.00           C  
HETATM   21  C20 UNL     1       0.525  -1.643   3.617  1.00  0.00           C  
HETATM   22  O2  UNL     1       1.648  -1.333   4.376  1.00  0.00           O  
HETATM   23  N1  UNL     1      -0.589  -1.420   1.505  1.00  0.00           N  
HETATM   24  C21 UNL     1      -1.429  -0.374   1.000  1.00  0.00           C  
HETATM   25  O3  UNL     1      -1.096   0.813   1.208  1.00  0.00           O  
HETATM   26  C22 UNL     1      -2.645  -0.708   0.259  1.00  0.00           C  
HETATM   27  C23 UNL     1      -3.377   0.477  -0.343  1.00  0.00           C  
HETATM   28  C24 UNL     1      -2.530   1.167  -1.340  1.00  0.00           C  
HETATM   29  C25 UNL     1      -3.048   2.367  -2.016  1.00  0.00           C  
HETATM   30  C26 UNL     1      -4.222   2.331  -2.883  1.00  0.00           C  
HETATM   31  C27 UNL     1      -5.541   1.903  -2.359  1.00  0.00           C  
HETATM   32  C28 UNL     1      -6.034   2.690  -1.198  1.00  0.00           C  
HETATM   33  C29 UNL     1      -7.410   2.159  -0.688  1.00  0.00           C  
HETATM   34  C30 UNL     1      -8.398   2.300  -1.763  1.00  0.00           C  
HETATM   35  C31 UNL     1      -9.805   1.986  -1.505  1.00  0.00           C  
HETATM   36  C32 UNL     1     -10.269   0.654  -1.111  1.00  0.00           C  
HETATM   37  C33 UNL     1      -9.847   0.161   0.223  1.00  0.00           C  
HETATM   38  C34 UNL     1     -10.436  -1.245   0.405  1.00  0.00           C  
HETATM   39  C35 UNL     1     -11.919  -1.193   0.349  1.00  0.00           C  
HETATM   40  C36 UNL     1     -12.436  -2.628   0.556  1.00  0.00           C  
HETATM   41  C37 UNL     1     -13.957  -2.526   0.490  1.00  0.00           C  
HETATM   42  C38 UNL     1     -14.376  -1.593   1.601  1.00  0.00           C  
HETATM   43  H1  UNL     1      14.669  -1.673   2.478  1.00  0.00           H  
HETATM   44  H2  UNL     1      14.129  -2.731   1.059  1.00  0.00           H  
HETATM   45  H3  UNL     1      15.660  -1.836   0.976  1.00  0.00           H  
HETATM   46  H4  UNL     1      14.737   0.249   0.810  1.00  0.00           H  
HETATM   47  H5  UNL     1      13.619  -0.711  -0.228  1.00  0.00           H  
HETATM   48  H6  UNL     1      12.424   0.836   1.375  1.00  0.00           H  
HETATM   49  H7  UNL     1      13.289   0.007   2.744  1.00  0.00           H  
HETATM   50  H8  UNL     1      11.056  -0.859   2.618  1.00  0.00           H  
HETATM   51  H9  UNL     1      12.292  -2.080   2.298  1.00  0.00           H  
HETATM   52  H10 UNL     1      10.348  -2.300   0.649  1.00  0.00           H  
HETATM   53  H11 UNL     1      11.900  -1.945  -0.173  1.00  0.00           H  
HETATM   54  H12 UNL     1      11.293   0.436  -0.259  1.00  0.00           H  
HETATM   55  H13 UNL     1      10.047  -0.654  -1.060  1.00  0.00           H  
HETATM   56  H14 UNL     1       8.698  -0.596   1.052  1.00  0.00           H  
HETATM   57  H15 UNL     1       9.874   0.512   1.781  1.00  0.00           H  
HETATM   58  H16 UNL     1       7.984   1.741   0.966  1.00  0.00           H  
HETATM   59  H17 UNL     1       9.526   2.160   0.067  1.00  0.00           H  
HETATM   60  H18 UNL     1       8.860   0.797  -1.800  1.00  0.00           H  
HETATM   61  H19 UNL     1       7.700   2.080  -1.472  1.00  0.00           H  
HETATM   62  H20 UNL     1       6.682  -0.120  -2.073  1.00  0.00           H  
HETATM   63  H21 UNL     1       7.541  -0.891  -0.685  1.00  0.00           H  
HETATM   64  H22 UNL     1       5.198  -0.553  -0.198  1.00  0.00           H  
HETATM   65  H23 UNL     1       6.224   0.384   0.931  1.00  0.00           H  
HETATM   66  H24 UNL     1       4.527   1.876   0.354  1.00  0.00           H  
HETATM   67  H25 UNL     1       5.935   2.417  -0.514  1.00  0.00           H  
HETATM   68  H26 UNL     1       4.127   2.604  -1.995  1.00  0.00           H  
HETATM   69  H27 UNL     1       5.454   1.528  -2.568  1.00  0.00           H  
HETATM   70  H28 UNL     1       3.445   0.623  -3.432  1.00  0.00           H  
HETATM   71  H29 UNL     1       4.113  -0.528  -2.221  1.00  0.00           H  
HETATM   72  H30 UNL     1       1.624  -0.253  -2.205  1.00  0.00           H  
HETATM   73  H31 UNL     1       1.772   1.401  -1.630  1.00  0.00           H  
HETATM   74  H32 UNL     1       2.891   0.501   0.568  1.00  0.00           H  
HETATM   75  H33 UNL     1       1.273  -1.715  -0.606  1.00  0.00           H  
HETATM   76  H34 UNL     1       1.728  -2.734   1.516  1.00  0.00           H  
HETATM   77  H35 UNL     1       3.373  -2.025   2.636  1.00  0.00           H  
HETATM   78  H36 UNL     1       0.701   0.036   2.237  1.00  0.00           H  
HETATM   79  H37 UNL     1      -0.403  -1.355   4.130  1.00  0.00           H  
HETATM   80  H38 UNL     1       0.517  -2.756   3.520  1.00  0.00           H  
HETATM   81  H39 UNL     1       1.720  -0.348   4.388  1.00  0.00           H  
HETATM   82  H40 UNL     1      -0.850  -2.414   1.349  1.00  0.00           H  
HETATM   83  H41 UNL     1      -3.316  -1.274   0.962  1.00  0.00           H  
HETATM   84  H42 UNL     1      -2.441  -1.458  -0.557  1.00  0.00           H  
HETATM   85  H43 UNL     1      -3.567   1.195   0.499  1.00  0.00           H  
HETATM   86  H44 UNL     1      -4.309   0.068  -0.744  1.00  0.00           H  
HETATM   87  H45 UNL     1      -1.569   1.486  -0.831  1.00  0.00           H  
HETATM   88  H46 UNL     1      -2.124   0.402  -2.099  1.00  0.00           H  
HETATM   89  H47 UNL     1      -3.097   3.189  -1.236  1.00  0.00           H  
HETATM   90  H48 UNL     1      -2.181   2.744  -2.670  1.00  0.00           H  
HETATM   91  H49 UNL     1      -4.325   3.321  -3.448  1.00  0.00           H  
HETATM   92  H50 UNL     1      -3.993   1.616  -3.749  1.00  0.00           H  
HETATM   93  H51 UNL     1      -6.276   2.214  -3.218  1.00  0.00           H  
HETATM   94  H52 UNL     1      -5.665   0.832  -2.342  1.00  0.00           H  
HETATM   95  H53 UNL     1      -5.350   2.560  -0.342  1.00  0.00           H  
HETATM   96  H54 UNL     1      -6.257   3.748  -1.443  1.00  0.00           H  
HETATM   97  H55 UNL     1      -7.669   2.756   0.193  1.00  0.00           H  
HETATM   98  H56 UNL     1      -7.207   1.105  -0.366  1.00  0.00           H  
HETATM   99  H57 UNL     1      -8.063   1.728  -2.702  1.00  0.00           H  
HETATM  100  H58 UNL     1      -8.362   3.380  -2.108  1.00  0.00           H  
HETATM  101  H59 UNL     1     -10.403   2.343  -2.434  1.00  0.00           H  
HETATM  102  H60 UNL     1     -10.141   2.770  -0.711  1.00  0.00           H  
HETATM  103  H61 UNL     1     -10.061  -0.120  -1.915  1.00  0.00           H  
HETATM  104  H62 UNL     1     -11.418   0.701  -1.166  1.00  0.00           H  
HETATM  105  H63 UNL     1      -8.809   0.177   0.492  1.00  0.00           H  
HETATM  106  H64 UNL     1     -10.369   0.752   1.052  1.00  0.00           H  
HETATM  107  H65 UNL     1     -10.135  -1.602   1.403  1.00  0.00           H  
HETATM  108  H66 UNL     1      -9.985  -1.864  -0.413  1.00  0.00           H  
HETATM  109  H67 UNL     1     -12.354  -0.895  -0.628  1.00  0.00           H  
HETATM  110  H68 UNL     1     -12.289  -0.512   1.119  1.00  0.00           H  
HETATM  111  H69 UNL     1     -12.095  -2.949   1.560  1.00  0.00           H  
HETATM  112  H70 UNL     1     -12.045  -3.253  -0.265  1.00  0.00           H  
HETATM  113  H71 UNL     1     -14.421  -3.514   0.534  1.00  0.00           H  
HETATM  114  H72 UNL     1     -14.171  -2.014  -0.495  1.00  0.00           H  
HETATM  115  H73 UNL     1     -15.390  -1.862   1.947  1.00  0.00           H  
HETATM  116  H74 UNL     1     -13.665  -1.660   2.465  1.00  0.00           H  
HETATM  117  H75 UNL     1     -14.352  -0.535   1.260  1.00  0.00           H  
CONECT    1    2   43   44   45
CONECT    2    3   46   47
CONECT    3    4   48   49
CONECT    4    5   50   51
CONECT    5    6   52   53
CONECT    6    7   54   55
CONECT    7    8   56   57
CONECT    8    9   58   59
CONECT    9   10   60   61
CONECT   10   11   62   63
CONECT   11   12   64   65
CONECT   12   13   66   67
CONECT   13   14   68   69
CONECT   14   15   70   71
CONECT   15   16   72   73
CONECT   16   17   17   74
CONECT   17   18   75
CONECT   18   19   20   76
CONECT   19   77
CONECT   20   21   23   78
CONECT   21   22   79   80
CONECT   22   81
CONECT   23   24   82
CONECT   24   25   25   26
CONECT   26   27   83   84
CONECT   27   28   85   86
CONECT   28   29   87   88
CONECT   29   30   89   90
CONECT   30   31   91   92
CONECT   31   32   93   94
CONECT   32   33   95   96
CONECT   33   34   97   98
CONECT   34   35   99  100
CONECT   35   36  101  102
CONECT   36   37  103  104
CONECT   37   38  105  106
CONECT   38   39  107  108
CONECT   39   40  109  110
CONECT   40   41  111  112
CONECT   41   42  113  114
CONECT   42  115  116  117
END

HMDB0240684
     RDKit          3D
Cer(d20:1/18:0)
117116  0  0  0  0  0  0  0  0999 V2000
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M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Cer D20:1/18:0	HMDB
Ceramide (D20:1,C18:0)	HMDB
Ceramide (D20:1/18:0)	HMDB
Ceramide(D20:1/18:0)	HMDB
N-Stearoyl-C20-sphingosine	HMDB
Ceramide	HMDB
N-(Octadecanoyl)-eicosasphing-4-enine	HMDB
N-(Octadecanoyl)-eicosasphingosine	HMDB
N-(Octadecanoyl)-eicosad-erythro-sphingosine	HMDB
N-(Octadecanoyl)-eicosa4-sphingenine	HMDB
N-(Octadecanoyl)-eicosad-sphingosine	HMDB
N-(Octadecanoyl)-eicosasphingenine	HMDB
N-(Octadecanoyl)-eicosaerythro-4-sphingenine	HMDB
Cer(d20:1/18:0)	HMDB

Chemical Formula

C₃₈H₇₅NO₃

Average Molecular Weight

594.022

Monoisotopic Molecular Weight

593.574695279

IUPAC Name

N-[(2S,3R,4E)-1,3-dihydroxyicos-4-en-2-yl]octadecanamide

Traditional Name

N-[(2S,3R,4E)-1,3-dihydroxyicos-4-en-2-yl]octadecanamide

CAS Registry Number

27888-43-3

SMILES

[H][C@@](CO)(NC(=O)CCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCCCC

InChI Identifier

InChI=1S/C38H75NO3/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-31-33-37(41)36(35-40)39-38(42)34-32-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h31,33,36-37,40-41H,3-30,32,34-35H2,1-2H3,(H,39,42)/b33-31+/t36-,37+/m0/s1

InChI Key

BDIIZHQNVIYLPJ-NUKVNZTCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as long-chain ceramides. These are ceramides bearing a long chain fatty acid.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Ceramides

Direct Parent

Long-chain ceramides

Alternative Parents

Substituents

Long-chain ceramide
Fatty amide
N-acyl-amine
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Carboxylic acid derivative
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Organic nitrogen compound
Carbonyl group
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Health effect

Insulin resistance (PMID: 24214972)
Diabetes mellitus (PMID: 17588815)
Neurodegenerative disease (PMID: 17588815)

Disposition

Biological location

Cellular substructure

Organelle

endoplasmic reticulum (PMID: 12408751)

golgi apparatus membrane (PMID: 12408751)
cell membrane (PMID: 12408751)

Cell

All cells and tissues (HMDB: HMDB0240684)

Process

Naturally occurring process

Apoptosis (PMID: 18216770)

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	10.01	ALOGPS
logP	12.64	ChemAxon
logS	-7.4	ALOGPS
pKa (Strongest Acidic)	13.62	ChemAxon
pKa (Strongest Basic)	-1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	69.56 Å²	ChemAxon
Rotatable Bond Count	34	ChemAxon
Refractivity	184.18 m³·mol⁻¹	ChemAxon
Polarizability	81.63 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	252.512	30932474
DeepCCS	[M-H]-	250.154	30932474
DeepCCS	[M-2H]-	283.921	30932474
DeepCCS	[M+Na]+	259.227	30932474
AllCCS	[M+H]+	268.7	32859911
AllCCS	[M+H-H2O]+	0.0	32859911
AllCCS	[M+NH4]+	270.1	32859911
AllCCS	[M+Na]+	270.4	32859911
AllCCS	[M-H]-	256.5	32859911
AllCCS	[M+Na-2H]-	0.0	32859911
AllCCS	[M+HCOO]-	261.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cer(d20:1/18:0)	[H][C@@](CO)(NC(=O)CCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCCCC	3617.8	Standard polar	33892256
Cer(d20:1/18:0)	[H][C@@](CO)(NC(=O)CCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCCCC	3946.7	Standard non polar	33892256
Cer(d20:1/18:0)	[H][C@@](CO)(NC(=O)CCCCCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCCCC	4658.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cer(d20:1/18:0),1TMS,isomer #1	CCCCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO[Si](C)(C)C)NC(=O)CCCCCCCCCCCCCCCCC	4537.2	Semi standard non polar	33892256
Cer(d20:1/18:0),1TMS,isomer #2	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](CO)NC(=O)CCCCCCCCCCCCCCCCC	4574.8	Semi standard non polar	33892256
Cer(d20:1/18:0),1TMS,isomer #3	CCCCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C	4430.2	Semi standard non polar	33892256
Cer(d20:1/18:0),2TMS,isomer #1	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](CO[Si](C)(C)C)NC(=O)CCCCCCCCCCCCCCCCC	4529.2	Semi standard non polar	33892256
Cer(d20:1/18:0),2TMS,isomer #2	CCCCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO[Si](C)(C)C)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C	4449.9	Semi standard non polar	33892256
Cer(d20:1/18:0),2TMS,isomer #3	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](CO)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C	4494.3	Semi standard non polar	33892256
Cer(d20:1/18:0),3TMS,isomer #1	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](CO[Si](C)(C)C)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C	4490.7	Semi standard non polar	33892256
Cer(d20:1/18:0),3TMS,isomer #1	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](CO[Si](C)(C)C)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C	4186.5	Standard non polar	33892256
Cer(d20:1/18:0),3TMS,isomer #1	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](CO[Si](C)(C)C)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C	4269.7	Standard polar	33892256
Cer(d20:1/18:0),1TBDMS,isomer #1	CCCCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO[Si](C)(C)C(C)(C)C)NC(=O)CCCCCCCCCCCCCCCCC	4778.6	Semi standard non polar	33892256
Cer(d20:1/18:0),1TBDMS,isomer #2	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO)NC(=O)CCCCCCCCCCCCCCCCC	4790.0	Semi standard non polar	33892256
Cer(d20:1/18:0),1TBDMS,isomer #3	CCCCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C	4673.6	Semi standard non polar	33892256
Cer(d20:1/18:0),2TBDMS,isomer #1	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO[Si](C)(C)C(C)(C)C)NC(=O)CCCCCCCCCCCCCCCCC	5043.4	Semi standard non polar	33892256
Cer(d20:1/18:0),2TBDMS,isomer #2	CCCCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO[Si](C)(C)C(C)(C)C)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C	4946.9	Semi standard non polar	33892256
Cer(d20:1/18:0),2TBDMS,isomer #3	CCCCCCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO)N(C(=O)CCCCCCCCCCCCCCCCC)[Si](C)(C)C(C)(C)C	4962.2	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS ("Cer(d20:1/18:0),1TMS,#1" TMS) - 70eV, Positive	Not Available	2021-10-14	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cer(d20:1/18:0) GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-10-15	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 10V, Positive-QTOF	splash10-0006-0000090000-e1e7c0e7cb968208dd58	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 20V, Positive-QTOF	splash10-0006-0050090000-ec7c3618689736711660	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 40V, Positive-QTOF	splash10-01r6-0075090000-095c8c6d755fb273be00	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 10V, Negative-QTOF	splash10-0006-0000090000-765c3bb6095a7a3d716d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 20V, Negative-QTOF	splash10-0006-0001090000-3215892fd017f8da2370	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 40V, Negative-QTOF	splash10-03do-0022090000-079b1227ac492b898d5a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 10V, Positive-QTOF	splash10-0udi-0000009000-ec17432a04610a853263	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 20V, Positive-QTOF	splash10-0udi-0000009000-ec17432a04610a853263	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cer(d20:1/18:0) 40V, Positive-QTOF	splash10-001i-0000091000-e707a6d11dfd3de1df01	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101853667

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Bowser PA, Gray GM: Sphingomyelinase in pig and human epidermis. J Invest Dermatol. 1978 Jun;70(6):331-5. [PubMed:25935 ]
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 ]

Showing metabocard for Cer(d20:1/18:0) (HMDB0240684)

MOL for HMDB0240684 (Cer(d20:1/18:0))

3D MOL for HMDB0240684 (Cer(d20:1/18:0))

3D SDF for HMDB0240684 (Cer(d20:1/18:0))

3D-SDF for HMDB0240684 (Cer(d20:1/18:0))

PDB for HMDB0240684 (Cer(d20:1/18:0))

3D PDB for HMDB0240684 (Cer(d20:1/18:0))

SMILES for HMDB0240684 (Cer(d20:1/18:0))

INCHI for HMDB0240684 (Cer(d20:1/18:0))

Structure for HMDB0240684 (Cer(d20:1/18:0))

3D Structure for HMDB0240684 (Cer(d20:1/18:0))

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra