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Record Information

Version

5.0

Status

Predicted

Creation Date

2021-09-17 12:30:14 UTC

Update Date

2022-11-30 20:08:27 UTC

HMDB ID

HMDB0293151

Secondary Accession Numbers

None

Metabolite Identification

Common Name

CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S))

Description

CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)) is an oxidized CDP-diacylglycerol (CDP-DG). Oxidized CDP-diacylglycerols are glycerophospholipids in which a cytidine diphosphate moiety occupies a glycerol substitution site and at least one of the fatty acyl chains has undergone oxidation. As all oxidized lipids, oxidized CDP-diacylglycerols belong to a group of biomolecules that have a role as signaling molecules. The biosynthesis of oxidized lipids is mediated by several enzymatic families, including cyclooxygenases (COX), lipoxygenases (LOX) and cytochrome P450s (CYP). Non-enzymatically oxidized lipids are produced by uncontrolled oxidation through free radicals and are considered harmful to human health (PMID: 33329396 ). As is the case with diacylglycerols, CDP-diacylglycerols can have many different combinations of fatty acids of varying lengths, saturation and degrees of oxidation attached at the C-1 and C-2 positions. CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)), in particular, consists of one chain of one 22-methyltetracosanoyl at the C-1 position and one chain of 14,15-epoxyeicosatrienoyl at the C-2 position. Phospholipids are ubiquitous in nature and are key components of the lipid bilayer of cells, as well as being involved in metabolism and signaling. Similarly to what occurs with phospholipids, the fatty acid distribution at the C-1 and C-2 positions of glycerol within oxidized phospholipids is continually in flux, owing to phospholipid degradation and the continuous phospholipid remodeling that occurs while these molecules are in membranes. Oxidized CDP-DGs can be synthesized via three different routes. In one route, the oxidized CDP-DG is synthetized de novo following the same mechanisms as for CDP-DGs but incorporating oxidized acyl chains (PMID: 33329396 ). An alternative is the transacylation of one of the non-oxidized acyl chains with an oxidized acylCoA (PMID: 33329396 ). The third pathway results from the oxidation of the acyl chain while still attached to the CDP-DG backbone, mainly through the action of LOX (PMID: 33329396 ).

Structure

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

CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S))
  Mrv1652309172114302D          

 79 81  0  0  1  0            999 V2000
   -3.8020    0.3607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0969    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -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 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8812   -1.0765    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0908   -1.0682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6217    0.7835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9068    0.3718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1918    0.7835    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.4769    0.3718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2442    0.7734    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9591    0.3596    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1552    1.4945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6703    1.4801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6057    1.5005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7802    1.5005    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1041   -0.4532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5359    2.0228    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1041    0.3706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8193    0.7836    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.8193    1.6096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1041    2.0226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3887    1.6096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3887    0.7836    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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    4.6714    0.3816    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4162   -0.4039    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5902   -0.4039    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3350    0.3816    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5121    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.3686    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0827    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.5109    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2250    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -11.6532    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -14.5097    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2239    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.9380    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.6521    0.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -20.2226    0.7695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.5095   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5095   -1.5126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2236   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9377   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6518   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3660   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1910   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9051   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6192   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4442   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1583   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8724   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6974   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4115   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.1256   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.1256   -1.5126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  -13.8397   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.5539   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2680   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -17.4104   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 32  1  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  3  5  1  1  0  0  0
  3  6  1  0  0  0  0
  4  3  1  0  0  0  0
  6 58  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
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 11 17  1  0  0  0  0
 11 18  2  0  0  0  0
 12 13  1  0  0  0  0
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 13 15  1  0  0  0  0
 13 16  2  0  0  0  0
 14  4  1  0  0  0  0
 21 22  1  0  0  0  0
 21 19  2  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 20  1  0  0  0  0
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 25 26  1  0  0  0  0
 26 21  1  0  0  0  0
 27 28  1  0  0  0  0
 27 31  1  0  0  0  0
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 28 26  1  1  0  0  0
 29 30  1  0  0  0  0
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 32 33  2  0  0  0  0
 32 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
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 78 79  1  0  0  0  0
M  END

HMDB0293151
     RDKit          3D
CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S))
177179  0  0  0  0  0  0  0  0999 V2000
   -7.9790    1.3698   -1.5338 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5885    1.9889   -1.5185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6071    0.8465   -1.4622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2180    1.3638   -1.4162 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8098    2.1875   -2.6364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3882    2.6159   -2.3386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6286    1.3112   -2.1608 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2139    2.2866   -3.0318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1053    1.9209   -4.5156 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3320    1.5955   -4.7913 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7349    0.4327   -5.1889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1782   -0.7014   -5.4257 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0695   -1.2799   -6.7895 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3896   -2.5672   -6.8541 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5262   -3.5123   -5.7473 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8503   -4.1487   -5.6022 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6604   -4.0821   -4.5656 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2845   -3.2994   -3.3695 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3429   -2.2354   -3.0404 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6487   -2.9301   -2.6331 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3344   -3.7180   -1.3888 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2910   -3.3965   -0.7027 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0734   -4.7619   -0.9371 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7189   -5.4805    0.2065 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6856   -5.6939    1.2753 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2011   -4.6083    1.9881 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4473   -3.6832    2.7038 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1715   -3.8280    2.6520 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9360   -2.5770    3.5128 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9408   -1.2048    3.0136 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6174   -0.6132    2.5522 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9056    0.8290    2.2225 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8467    1.6415    1.6262 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5413    1.7437    2.3429 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7403    2.2676    3.7460 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4400    2.3398    4.4865 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5256    3.3697    3.8779 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0331    4.7627    4.0747 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2114    5.8678    3.5138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2438    5.8458    3.9307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9673    7.0701    3.4499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8696    7.4100    2.0309 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3069    6.4025    1.0006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0522    7.0535   -0.3616 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3086    6.2380   -1.5394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6607    5.7088   -1.7956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7580    6.7395   -1.9367 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0203    5.9215   -2.3023 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1506    6.8843   -2.4739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3912    7.6201   -1.1876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4061    6.2328   -2.9613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8826    5.1797   -2.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9847   -6.7690   -0.1992 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7115   -7.6151   -0.9865 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7436   -8.9871   -1.3818 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.4916   -8.4659   -2.0846 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5775   -9.9848   -2.4332 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2282   -9.7670    0.0101 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5679   -9.9679    0.1085 P   0  0  0  0  0  5  0  0  0  0  0  0
    0.9411   -9.9174   -1.2828 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1570  -11.4262    0.8696 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8062   -8.7234    1.0108 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1312   -9.2712    1.8582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8742   -8.2837    2.7030 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END

CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S))
  Mrv1652309172114302D          

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M  END
> <DATABASE_ID>
HMDB0293151

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CCCCCCCCCCCCCCCCCCCCC(C)CC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCC\C=C/C\C=C/C\C=C/CC1OC1CCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C57H99N3O16P2/c1-4-6-31-37-48-49(74-48)38-33-28-24-20-17-18-22-26-30-35-40-53(62)73-47(43-70-52(61)39-34-29-25-21-16-14-12-10-8-7-9-11-13-15-19-23-27-32-36-46(3)5-2)44-71-77(66,67)76-78(68,69)72-45-50-54(63)55(64)56(75-50)60-42-41-51(58)59-57(60)65/h17,20,22,26,28,33,41-42,46-50,54-56,63-64H,4-16,18-19,21,23-25,27,29-32,34-40,43-45H2,1-3H3,(H,66,67)(H,68,69)(H2,58,59,65)/b20-17-,26-22-,33-28-/t46?,47-,48?,49?,50-,54-,55-,56-/m1/s1

> <INCHI_KEY>
DKYIHROBEULIGN-LFAYAAJWSA-N

> <FORMULA>
C57H99N3O16P2

> <MOLECULAR_WEIGHT>
1144.372

> <EXACT_MASS>
1143.650058116

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
177

> <JCHEM_AVERAGE_POLARIZABILITY>
128.1095306221084

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(22-methyltetracosanoyl)oxy]-2-{[(5Z,8Z,11Z)-13-(3-pentyloxiran-2-yl)trideca-5,8,11-trienoyl]oxy}propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
7.98

> <JCHEM_LOGP>
12.79290932333333

> <ALOGPS_LOGS>
-6.29

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.271625568103402

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8631677225718377

> <JCHEM_PKA_STRONGEST_BASIC>
-0.031961141968606666

> <JCHEM_POLAR_SURFACE_AREA>
275.8

> <JCHEM_REFRACTIVITY>
302.8418

> <JCHEM_ROTATABLE_BOND_COUNT>
50

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.84e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-[(22-methyltetracosanoyl)oxy]-2-{[(5Z,8Z,11Z)-13-(3-pentyloxiran-2-yl)trideca-5,8,11-trienoyl]oxy}propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0293151
     RDKit          3D
CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S))
177179  0  0  0  0  0  0  0  0999 V2000
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   -6.5885    1.9889   -1.5185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6071    0.8465   -1.4622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2180    1.3638   -1.4162 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

HEADER    PROTEIN                                 17-SEP-21   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S))         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-21         0                                  
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HETATM   68  C   UNK     0     -18.962  -0.612   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0     -20.295  -1.383   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0     -21.835  -1.383   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0     -23.168  -0.612   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0     -24.501  -1.383   0.000  0.00  0.00           C+0
HETATM   73  O   UNK     0     -24.501  -2.823   0.000  0.00  0.00           O+0
HETATM   74  C   UNK     0     -25.834  -0.612   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0     -27.167  -1.383   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0     -28.500  -0.612   0.000  0.00  0.00           C+0
HETATM   77  C   UNK     0     -29.833  -1.383   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0     -31.166  -0.612   0.000  0.00  0.00           C+0
HETATM   79  C   UNK     0     -32.499  -1.383   0.000  0.00  0.00           C+0
CONECT    1   32    2                                                       
CONECT    2    1    3                                                       
CONECT    3    2    5    6    4                                             
CONECT    4    3   14                                                       
CONECT    5    3                                                            
CONECT    6    3   58                                                       
CONECT    7   29                                                            
CONECT    8   30                                                            
CONECT    9   10   31                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   17   18                                             
CONECT   12   11   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13    4                                                       
CONECT   15   13                                                            
CONECT   16   13                                                            
CONECT   17   11                                                            
CONECT   18   11                                                            
CONECT   19   21                                                            
CONECT   20   23                                                            
CONECT   21   22   19   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   20                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   21   28                                                  
CONECT   27   28   31                                                       
CONECT   28   27   29   26                                                  
CONECT   29   28   30    7                                                  
CONECT   30   29   31    8                                                  
CONECT   31   27   30    9                                                  
CONECT   32    1   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   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   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54   57                                                       
CONECT   57   56                                                            
CONECT   58    6   59   60                                                  
CONECT   59   58                                                            
CONECT   60   58   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69                                                       
CONECT   69   68   70                                                       
CONECT   70   69   71                                                       
CONECT   71   70   72                                                       
CONECT   72   71   73   74                                                  
CONECT   73   72   74                                                       
CONECT   74   72   73   75                                                  
CONECT   75   74   76                                                       
CONECT   76   75   77                                                       
CONECT   77   76   78                                                       
CONECT   78   77   79                                                       
CONECT   79   78                                                            
MASTER        0    0    0    0    0    0    0    0   79    0  162    0
END

COMPND    HMDB0293151
HETATM    1  C1  UNL     1      -7.979   1.370  -1.534  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.589   1.989  -1.519  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.607   0.846  -1.462  1.00  0.00           C  
HETATM    4  C4  UNL     1      -4.218   1.364  -1.416  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.810   2.187  -2.636  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.388   2.616  -2.339  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.629   1.311  -2.161  1.00  0.00           O  
HETATM    8  C7  UNL     1      -1.214   2.287  -3.032  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.105   1.921  -4.516  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.332   1.596  -4.791  1.00  0.00           C  
HETATM   11  C10 UNL     1       0.735   0.433  -5.189  1.00  0.00           C  
HETATM   12  C11 UNL     1      -0.178  -0.701  -5.426  1.00  0.00           C  
HETATM   13  C12 UNL     1       0.070  -1.280  -6.789  1.00  0.00           C  
HETATM   14  C13 UNL     1       0.390  -2.567  -6.854  1.00  0.00           C  
HETATM   15  C14 UNL     1       0.526  -3.512  -5.747  1.00  0.00           C  
HETATM   16  C15 UNL     1       1.850  -4.149  -5.602  1.00  0.00           C  
HETATM   17  C16 UNL     1       2.660  -4.082  -4.566  1.00  0.00           C  
HETATM   18  C17 UNL     1       2.285  -3.299  -3.370  1.00  0.00           C  
HETATM   19  C18 UNL     1       3.343  -2.235  -3.040  1.00  0.00           C  
HETATM   20  C19 UNL     1       4.649  -2.930  -2.633  1.00  0.00           C  
HETATM   21  C20 UNL     1       4.334  -3.718  -1.389  1.00  0.00           C  
HETATM   22  O2  UNL     1       3.291  -3.397  -0.703  1.00  0.00           O  
HETATM   23  O3  UNL     1       5.073  -4.762  -0.937  1.00  0.00           O  
HETATM   24  C21 UNL     1       4.719  -5.480   0.206  1.00  0.00           C  
HETATM   25  C22 UNL     1       5.686  -5.694   1.275  1.00  0.00           C  
HETATM   26  O4  UNL     1       6.201  -4.608   1.988  1.00  0.00           O  
HETATM   27  C23 UNL     1       5.447  -3.683   2.704  1.00  0.00           C  
HETATM   28  O5  UNL     1       4.172  -3.828   2.652  1.00  0.00           O  
HETATM   29  C24 UNL     1       5.936  -2.577   3.513  1.00  0.00           C  
HETATM   30  C25 UNL     1       5.941  -1.205   3.014  1.00  0.00           C  
HETATM   31  C26 UNL     1       4.617  -0.613   2.552  1.00  0.00           C  
HETATM   32  C27 UNL     1       4.906   0.829   2.223  1.00  0.00           C  
HETATM   33  C28 UNL     1       3.847   1.641   1.626  1.00  0.00           C  
HETATM   34  C29 UNL     1       2.541   1.744   2.343  1.00  0.00           C  
HETATM   35  C30 UNL     1       2.740   2.268   3.746  1.00  0.00           C  
HETATM   36  C31 UNL     1       1.440   2.340   4.487  1.00  0.00           C  
HETATM   37  C32 UNL     1       0.526   3.370   3.878  1.00  0.00           C  
HETATM   38  C33 UNL     1       1.033   4.763   4.075  1.00  0.00           C  
HETATM   39  C34 UNL     1       0.211   5.868   3.514  1.00  0.00           C  
HETATM   40  C35 UNL     1      -1.244   5.846   3.931  1.00  0.00           C  
HETATM   41  C36 UNL     1      -1.967   7.070   3.450  1.00  0.00           C  
HETATM   42  C37 UNL     1      -1.870   7.410   2.031  1.00  0.00           C  
HETATM   43  C38 UNL     1      -2.307   6.402   1.001  1.00  0.00           C  
HETATM   44  C39 UNL     1      -2.052   7.053  -0.362  1.00  0.00           C  
HETATM   45  C40 UNL     1      -2.309   6.238  -1.539  1.00  0.00           C  
HETATM   46  C41 UNL     1      -3.661   5.709  -1.796  1.00  0.00           C  
HETATM   47  C42 UNL     1      -4.758   6.739  -1.937  1.00  0.00           C  
HETATM   48  C43 UNL     1      -6.020   5.921  -2.302  1.00  0.00           C  
HETATM   49  C44 UNL     1      -7.151   6.884  -2.474  1.00  0.00           C  
HETATM   50  C45 UNL     1      -7.391   7.620  -1.188  1.00  0.00           C  
HETATM   51  C46 UNL     1      -8.406   6.233  -2.961  1.00  0.00           C  
HETATM   52  C47 UNL     1      -8.883   5.180  -2.002  1.00  0.00           C  
HETATM   53  C48 UNL     1       3.985  -6.769  -0.199  1.00  0.00           C  
HETATM   54  O6  UNL     1       4.712  -7.615  -0.986  1.00  0.00           O  
HETATM   55  P1  UNL     1       3.744  -8.987  -1.382  1.00  0.00           P  
HETATM   56  O7  UNL     1       2.492  -8.466  -2.085  1.00  0.00           O  
HETATM   57  O8  UNL     1       4.577  -9.985  -2.433  1.00  0.00           O  
HETATM   58  O9  UNL     1       3.228  -9.767   0.010  1.00  0.00           O  
HETATM   59  P2  UNL     1       1.568  -9.968   0.108  1.00  0.00           P  
HETATM   60  O10 UNL     1       0.941  -9.917  -1.283  1.00  0.00           O  
HETATM   61  O11 UNL     1       1.157 -11.426   0.870  1.00  0.00           O  
HETATM   62  O12 UNL     1       0.806  -8.723   1.011  1.00  0.00           O  
HETATM   63  C49 UNL     1      -0.131  -9.271   1.858  1.00  0.00           C  
HETATM   64  C50 UNL     1      -0.874  -8.284   2.703  1.00  0.00           C  
HETATM   65  O13 UNL     1       0.012  -7.565   3.514  1.00  0.00           O  
HETATM   66  C51 UNL     1      -0.736  -6.452   3.938  1.00  0.00           C  
HETATM   67  N1  UNL     1       0.120  -5.406   4.438  1.00  0.00           N  
HETATM   68  C52 UNL     1      -0.401  -4.251   4.864  1.00  0.00           C  
HETATM   69  C53 UNL     1       0.409  -3.224   5.356  1.00  0.00           C  
HETATM   70  C54 UNL     1       1.761  -3.483   5.372  1.00  0.00           C  
HETATM   71  N2  UNL     1       2.610  -2.441   5.874  1.00  0.00           N  
HETATM   72  N3  UNL     1       2.237  -4.655   4.936  1.00  0.00           N  
HETATM   73  C55 UNL     1       1.450  -5.619   4.471  1.00  0.00           C  
HETATM   74  O14 UNL     1       1.939  -6.725   4.059  1.00  0.00           O  
HETATM   75  C56 UNL     1      -1.591  -6.060   2.777  1.00  0.00           C  
HETATM   76  O15 UNL     1      -2.937  -5.865   3.163  1.00  0.00           O  
HETATM   77  C57 UNL     1      -1.556  -7.261   1.852  1.00  0.00           C  
HETATM   78  O16 UNL     1      -2.845  -7.695   1.533  1.00  0.00           O  
HETATM   79  H1  UNL     1      -7.947   0.403  -1.004  1.00  0.00           H  
HETATM   80  H2  UNL     1      -8.649   2.072  -1.004  1.00  0.00           H  
HETATM   81  H3  UNL     1      -8.351   1.277  -2.584  1.00  0.00           H  
HETATM   82  H4  UNL     1      -6.391   2.575  -2.439  1.00  0.00           H  
HETATM   83  H5  UNL     1      -6.419   2.642  -0.655  1.00  0.00           H  
HETATM   84  H6  UNL     1      -5.687   0.205  -2.385  1.00  0.00           H  
HETATM   85  H7  UNL     1      -5.779   0.190  -0.582  1.00  0.00           H  
HETATM   86  H8  UNL     1      -4.006   2.024  -0.531  1.00  0.00           H  
HETATM   87  H9  UNL     1      -3.446   0.560  -1.329  1.00  0.00           H  
HETATM   88  H10 UNL     1      -3.871   1.548  -3.552  1.00  0.00           H  
HETATM   89  H11 UNL     1      -4.481   3.039  -2.703  1.00  0.00           H  
HETATM   90  H12 UNL     1      -2.314   3.096  -1.331  1.00  0.00           H  
HETATM   91  H13 UNL     1      -0.262   2.804  -2.696  1.00  0.00           H  
HETATM   92  H14 UNL     1      -1.349   2.896  -5.034  1.00  0.00           H  
HETATM   93  H15 UNL     1      -1.837   1.217  -4.823  1.00  0.00           H  
HETATM   94  H16 UNL     1       1.078   2.404  -4.648  1.00  0.00           H  
HETATM   95  H17 UNL     1       1.810   0.247  -5.379  1.00  0.00           H  
HETATM   96  H18 UNL     1       0.016  -1.442  -4.676  1.00  0.00           H  
HETATM   97  H19 UNL     1      -1.259  -0.402  -5.476  1.00  0.00           H  
HETATM   98  H20 UNL     1      -0.011  -0.664  -7.670  1.00  0.00           H  
HETATM   99  H21 UNL     1       0.583  -2.969  -7.868  1.00  0.00           H  
HETATM  100  H22 UNL     1       0.006  -3.276  -4.816  1.00  0.00           H  
HETATM  101  H23 UNL     1      -0.129  -4.423  -6.115  1.00  0.00           H  
HETATM  102  H24 UNL     1       2.211  -4.757  -6.457  1.00  0.00           H  
HETATM  103  H25 UNL     1       3.625  -4.617  -4.597  1.00  0.00           H  
HETATM  104  H26 UNL     1       2.158  -3.998  -2.513  1.00  0.00           H  
HETATM  105  H27 UNL     1       1.367  -2.740  -3.544  1.00  0.00           H  
HETATM  106  H28 UNL     1       3.493  -1.567  -3.888  1.00  0.00           H  
HETATM  107  H29 UNL     1       2.972  -1.675  -2.172  1.00  0.00           H  
HETATM  108  H30 UNL     1       5.334  -2.130  -2.307  1.00  0.00           H  
HETATM  109  H31 UNL     1       5.034  -3.533  -3.437  1.00  0.00           H  
HETATM  110  H32 UNL     1       3.836  -4.902   0.665  1.00  0.00           H  
HETATM  111  H33 UNL     1       6.588  -6.206   0.821  1.00  0.00           H  
HETATM  112  H34 UNL     1       5.234  -6.388   2.040  1.00  0.00           H  
HETATM  113  H35 UNL     1       5.444  -2.589   4.555  1.00  0.00           H  
HETATM  114  H36 UNL     1       7.014  -2.817   3.811  1.00  0.00           H  
HETATM  115  H37 UNL     1       6.630  -1.141   2.115  1.00  0.00           H  
HETATM  116  H38 UNL     1       6.334  -0.528   3.811  1.00  0.00           H  
HETATM  117  H39 UNL     1       3.879  -0.694   3.369  1.00  0.00           H  
HETATM  118  H40 UNL     1       4.277  -1.205   1.697  1.00  0.00           H  
HETATM  119  H41 UNL     1       5.242   1.326   3.190  1.00  0.00           H  
HETATM  120  H42 UNL     1       5.794   0.866   1.529  1.00  0.00           H  
HETATM  121  H43 UNL     1       3.667   1.371   0.531  1.00  0.00           H  
HETATM  122  H44 UNL     1       4.271   2.698   1.518  1.00  0.00           H  
HETATM  123  H45 UNL     1       1.846   2.430   1.764  1.00  0.00           H  
HETATM  124  H46 UNL     1       1.993   0.784   2.387  1.00  0.00           H  
HETATM  125  H47 UNL     1       3.284   3.220   3.659  1.00  0.00           H  
HETATM  126  H48 UNL     1       3.451   1.561   4.237  1.00  0.00           H  
HETATM  127  H49 UNL     1       0.917   1.378   4.478  1.00  0.00           H  
HETATM  128  H50 UNL     1       1.655   2.669   5.548  1.00  0.00           H  
HETATM  129  H51 UNL     1      -0.458   3.251   4.437  1.00  0.00           H  
HETATM  130  H52 UNL     1       0.304   3.087   2.851  1.00  0.00           H  
HETATM  131  H53 UNL     1       2.064   4.848   3.612  1.00  0.00           H  
HETATM  132  H54 UNL     1       1.226   4.921   5.156  1.00  0.00           H  
HETATM  133  H55 UNL     1       0.604   6.843   3.910  1.00  0.00           H  
HETATM  134  H56 UNL     1       0.249   5.952   2.410  1.00  0.00           H  
HETATM  135  H57 UNL     1      -1.770   4.976   3.429  1.00  0.00           H  
HETATM  136  H58 UNL     1      -1.350   5.808   5.036  1.00  0.00           H  
HETATM  137  H59 UNL     1      -1.710   7.959   4.077  1.00  0.00           H  
HETATM  138  H60 UNL     1      -3.067   6.905   3.679  1.00  0.00           H  
HETATM  139  H61 UNL     1      -0.848   7.827   1.756  1.00  0.00           H  
HETATM  140  H62 UNL     1      -2.546   8.312   1.862  1.00  0.00           H  
HETATM  141  H63 UNL     1      -1.800   5.435   1.086  1.00  0.00           H  
HETATM  142  H64 UNL     1      -3.384   6.255   1.090  1.00  0.00           H  
HETATM  143  H65 UNL     1      -0.987   7.393  -0.339  1.00  0.00           H  
HETATM  144  H66 UNL     1      -2.636   8.023  -0.421  1.00  0.00           H  
HETATM  145  H67 UNL     1      -2.023   6.848  -2.452  1.00  0.00           H  
HETATM  146  H68 UNL     1      -1.605   5.350  -1.590  1.00  0.00           H  
HETATM  147  H69 UNL     1      -3.629   5.205  -2.814  1.00  0.00           H  
HETATM  148  H70 UNL     1      -3.975   4.875  -1.116  1.00  0.00           H  
HETATM  149  H71 UNL     1      -4.997   7.251  -0.974  1.00  0.00           H  
HETATM  150  H72 UNL     1      -4.511   7.473  -2.699  1.00  0.00           H  
HETATM  151  H73 UNL     1      -5.829   5.300  -3.211  1.00  0.00           H  
HETATM  152  H74 UNL     1      -6.207   5.295  -1.394  1.00  0.00           H  
HETATM  153  H75 UNL     1      -6.820   7.635  -3.257  1.00  0.00           H  
HETATM  154  H76 UNL     1      -6.929   8.608  -1.230  1.00  0.00           H  
HETATM  155  H77 UNL     1      -8.501   7.679  -0.985  1.00  0.00           H  
HETATM  156  H78 UNL     1      -6.918   7.081  -0.339  1.00  0.00           H  
HETATM  157  H79 UNL     1      -9.170   7.044  -3.082  1.00  0.00           H  
HETATM  158  H80 UNL     1      -8.227   5.749  -3.952  1.00  0.00           H  
HETATM  159  H81 UNL     1      -8.044   4.498  -1.772  1.00  0.00           H  
HETATM  160  H82 UNL     1      -9.344   5.607  -1.097  1.00  0.00           H  
HETATM  161  H83 UNL     1      -9.626   4.519  -2.549  1.00  0.00           H  
HETATM  162  H84 UNL     1       3.698  -7.267   0.735  1.00  0.00           H  
HETATM  163  H85 UNL     1       3.069  -6.439  -0.740  1.00  0.00           H  
HETATM  164  H86 UNL     1       4.042 -10.290  -3.206  1.00  0.00           H  
HETATM  165  H87 UNL     1       1.843 -12.108   0.815  1.00  0.00           H  
HETATM  166  H88 UNL     1       0.407 -10.012   2.516  1.00  0.00           H  
HETATM  167  H89 UNL     1      -0.850  -9.861   1.240  1.00  0.00           H  
HETATM  168  H90 UNL     1      -1.589  -8.794   3.402  1.00  0.00           H  
HETATM  169  H91 UNL     1      -1.418  -6.854   4.732  1.00  0.00           H  
HETATM  170  H92 UNL     1      -1.463  -4.053   4.843  1.00  0.00           H  
HETATM  171  H93 UNL     1      -0.021  -2.293   5.696  1.00  0.00           H  
HETATM  172  H94 UNL     1       2.446  -1.467   5.574  1.00  0.00           H  
HETATM  173  H95 UNL     1       3.352  -2.718   6.518  1.00  0.00           H  
HETATM  174  H96 UNL     1      -1.257  -5.163   2.243  1.00  0.00           H  
HETATM  175  H97 UNL     1      -3.062  -6.334   4.026  1.00  0.00           H  
HETATM  176  H98 UNL     1      -0.964  -7.026   0.967  1.00  0.00           H  
HETATM  177  H99 UNL     1      -2.764  -8.583   1.136  1.00  0.00           H  
CONECT    1    2   79   80   81
CONECT    2    3   82   83
CONECT    3    4   84   85
CONECT    4    5   86   87
CONECT    5    6   88   89
CONECT    6    7    8   90
CONECT    7    8
CONECT    8    9   91
CONECT    9   10   92   93
CONECT   10   11   11   94
CONECT   11   12   95
CONECT   12   13   96   97
CONECT   13   14   14   98
CONECT   14   15   99
CONECT   15   16  100  101
CONECT   16   17   17  102
CONECT   17   18  103
CONECT   18   19  104  105
CONECT   19   20  106  107
CONECT   20   21  108  109
CONECT   21   22   22   23
CONECT   23   24
CONECT   24   25   53  110
CONECT   25   26  111  112
CONECT   26   27
CONECT   27   28   28   29
CONECT   29   30  113  114
CONECT   30   31  115  116
CONECT   31   32  117  118
CONECT   32   33  119  120
CONECT   33   34  121  122
CONECT   34   35  123  124
CONECT   35   36  125  126
CONECT   36   37  127  128
CONECT   37   38  129  130
CONECT   38   39  131  132
CONECT   39   40  133  134
CONECT   40   41  135  136
CONECT   41   42  137  138
CONECT   42   43  139  140
CONECT   43   44  141  142
CONECT   44   45  143  144
CONECT   45   46  145  146
CONECT   46   47  147  148
CONECT   47   48  149  150
CONECT   48   49  151  152
CONECT   49   50   51  153
CONECT   50  154  155  156
CONECT   51   52  157  158
CONECT   52  159  160  161
CONECT   53   54  162  163
CONECT   54   55
CONECT   55   56   56   57   58
CONECT   57  164
CONECT   58   59
CONECT   59   60   60   61   62
CONECT   61  165
CONECT   62   63
CONECT   63   64  166  167
CONECT   64   65   77  168
CONECT   65   66
CONECT   66   67   75  169
CONECT   67   68   73
CONECT   68   69   69  170
CONECT   69   70  171
CONECT   70   71   72   72
CONECT   71  172  173
CONECT   72   73
CONECT   73   74   74
CONECT   75   76   77  174
CONECT   76  175
CONECT   77   78  176
CONECT   78  177
END

HMDB0293151
     RDKit          3D
CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S))
177179  0  0  0  0  0  0  0  0999 V2000
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    1.8434  -12.1084    0.8149 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4072  -10.0123    2.5164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8502   -9.8605    1.2402 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4176   -6.8544    4.7324 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4627   -4.0534    4.8434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0210   -2.2926    5.6961 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4456   -1.4673    5.5741 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -2.7176    6.5177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2570   -5.1634    2.2431 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0623   -6.3342    4.0260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9641   -7.0256    0.9674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639   -8.5826    1.1359 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(22-methyltetracosanoyl)oxy]-2-{[(5Z,8Z,11Z)-13-(3-pentyloxiran-2-yl)trideca-5,8,11-trienoyl]oxy}propoxy]phosphoryl}oxy)phosphinate	Generator

Chemical Formula

C₅₇H₉₉N₃O₁₆P₂

Average Molecular Weight

1144.372

Monoisotopic Molecular Weight

1143.650058116

IUPAC Name

{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(22-methyltetracosanoyl)oxy]-2-{[(5Z,8Z,11Z)-13-(3-pentyloxiran-2-yl)trideca-5,8,11-trienoyl]oxy}propoxy]phosphoryl}oxy)phosphinic acid

Traditional Name

[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-[(22-methyltetracosanoyl)oxy]-2-{[(5Z,8Z,11Z)-13-(3-pentyloxiran-2-yl)trideca-5,8,11-trienoyl]oxy}propoxy)phosphoryl]oxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](COC(=O)CCCCCCCCCCCCCCCCCCCCC(C)CC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCC\C=C/C\C=C/C\C=C/CC1OC1CCCCC

InChI Identifier

InChI=1S/C57H99N3O16P2/c1-4-6-31-37-48-49(74-48)38-33-28-24-20-17-18-22-26-30-35-40-53(62)73-47(43-70-52(61)39-34-29-25-21-16-14-12-10-8-7-9-11-13-15-19-23-27-32-36-46(3)5-2)44-71-77(66,67)76-78(68,69)72-45-50-54(63)55(64)56(75-50)60-42-41-51(58)59-57(60)65/h17,20,22,26,28,33,41-42,46-50,54-56,63-64H,4-16,18-19,21,23-25,27,29-32,34-40,43-45H2,1-3H3,(H,66,67)(H,68,69)(H2,58,59,65)/b20-17-,26-22-,33-28-/t46?,47-,48?,49?,50-,54-,55-,56-/m1/s1

InChI Key

DKYIHROBEULIGN-LFAYAAJWSA-N

Chemical Taxonomy

Classification

Not classified

Ontology

Not Available

Endogenous (HMDB: HMDB0293151)

Process

Not Available

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	7.98	ALOGPS
logP	12.79	ChemAxon
logS	-6.3	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-0.032	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	275.8 Å²	ChemAxon
Rotatable Bond Count	50	ChemAxon
Refractivity	302.84 m³·mol⁻¹	ChemAxon
Polarizability	128.11 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	329.367	32859911
AllCCS	[M+H-H2O]+	329.743	32859911
AllCCS	[M+Na]+	328.882	32859911
AllCCS	[M+NH4]+	328.994	32859911
AllCCS	[M-H]-	298.658	32859911
AllCCS	[M+Na-2H]-	304.418	32859911
AllCCS	[M+HCOO]-	310.619	32859911
DeepCCS	[M+H]+	292.56	30932474
DeepCCS	[M-H]-	290.907	30932474
DeepCCS	[M-2H]-	324.942	30932474
DeepCCS	[M+Na]+	298.717	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	8.62 minutes	32390414
Predicted by Siyang on May 30, 2022	30.5437 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.98 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	5876.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	178.8 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	387.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	204.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	1236.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	1890.3 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	1374.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	319.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	3273.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	1386.1 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	3045.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	1288.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	770.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	154.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	350.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	11.4 seconds	40023050

Predicted Kovats Retention Indices

Not Available

Spectra

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

Not Available

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

Hajeyah AA, Griffiths WJ, Wang Y, Finch AJ, O'Donnell VB: The Biosynthesis of Enzymatically Oxidized Lipids. Front Endocrinol (Lausanne). 2020 Nov 19;11:591819. doi: 10.3389/fendo.2020.591819. eCollection 2020. [PubMed:33329396 ]

Showing metabocard for CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)) (HMDB0293151)

MOL for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

3D MOL for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

3D SDF for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

3D-SDF for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

PDB for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

3D PDB for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

SMILES for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

INCHI for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

Structure for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

3D Structure for HMDB0293151 (CDP-DG(a-25:0/20:3(5Z,8Z,11Z)-O(14R,15S)))

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices