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Showing metabocard for CDP-DG(20:3(5Z,8Z,11Z)/PGJ2) (HMDB0291939)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 03:37:39 UTC
Update Date2022-11-30 20:07:50 UTC
HMDB IDHMDB0291939
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(20:3(5Z,8Z,11Z)/PGJ2)
DescriptionCDP-DG(20:3(5Z,8Z,11Z)/PGJ2) 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(20:3(5Z,8Z,11Z)/PGJ2), in particular, consists of one chain of one 5Z,8Z,11Z-eicosatrienoyl at the C-1 position and one chain of Prostaglandin J2 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0291939 (CDP-DG(20:3(5Z,8Z,11Z)/PGJ2))


  Mrv1652309172105382D          

 74 76  0  0  1  0            999 V2000
    7.8702   -8.6271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.4624   -7.8750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6379   -7.8469    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.2500   -7.1187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5259   -7.5918    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6866   -6.4188    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5111   -6.4469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8990   -7.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2987   -5.6906    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4770   -5.9287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
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3D MOL for HMDB0291939 (CDP-DG(20:3(5Z,8Z,11Z)/PGJ2))

HMDB0291939
     RDKit          3D
CDP-DG(20:3(5Z,8Z,11Z)/PGJ2)
155157  0  0  0  0  0  0  0  0999 V2000
   15.9317   -0.6303    4.0206 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9251   -0.7410    2.4774 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2101   -0.2634    1.9344 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5752   -0.3031    0.5333 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8913    0.3331   -0.5814 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6151   -0.0377   -1.1671 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3530   -0.0739   -0.4325 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1638   -0.4080   -1.3707 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9881    0.5515   -2.4454 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9810    1.3271   -2.6901 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7216    1.4932   -1.9786 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4502    0.7742   -0.7535 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4699   -0.1086   -0.5959 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.1347   -0.2167   -1.4413 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.0456    1.0013    0.7397 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6050    0.3801    2.0270 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1548    0.2612    2.2774 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4823   -0.7056    1.4079 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1235   -1.6090    0.7847 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0957   -0.6865    1.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5051   -1.6462    0.3758 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0221   -1.4083    0.3094 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3872   -1.3549    1.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -12.2191    0.3677    1.2347 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6375   -0.0811    1.1730 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -16.3687    0.5472    1.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0348    0.9097    2.2660 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.8944    1.7875    1.6431 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7892    0.8411    1.3852 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6400    1.2391    2.0594 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1965   -1.6638   -1.2852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7504   -2.5045   -2.4058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5518   -2.4083   -2.9721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7565   -1.1589   -3.0179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7150   -1.0831   -1.9508 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0291939 (CDP-DG(20:3(5Z,8Z,11Z)/PGJ2))


  Mrv1652309172105382D          

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 61 73  1  0  0  0  0
 73 74  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0291939

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCC\C=C/C\C=C/C\C=C/CCCC(=O)OC[C@@H]1COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@@H](CC=CCCCC(=O)O1)C=CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@H](O)[C@@H]2O)N1C=CC(N)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C52H81N3O17P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-19-20-25-29-47(58)67-37-42-38-68-73(63,64)72-74(65,66)69-39-45-50(61)49(60)43(33-32-41(56)28-23-6-4-2)44(57)34-31-40(27-24-21-22-26-30-48(59)70-42)51(71-45)55-36-35-46(53)54-52(55)62/h12-13,15-16,18-19,21,24,31-36,40-43,45,49-51,56,60-61H,3-11,14,17,20,22-23,25-30,37-39H2,1-2H3,(H,63,64)(H,65,66)(H2,53,54,62)/b13-12-,16-15-,19-18-,24-21-,33-32+,34-31?/t40-,41?,42+,43-,45+,49-,50+,51+/m0/s1

> <INCHI_KEY>
PQLKYSWBDHQISO-IVMRCEIQSA-N

> <FORMULA>
C52H81N3O17P2

> <MOLECULAR_WEIGHT>
1082.172

> <EXACT_MASS>
1081.504122156

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
155

> <JCHEM_AVERAGE_POLARIZABILITY>
115.71649364702643

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1R,9R,15Z,18S,22R,23S,24S,26R)-26-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,23,24-tetrahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,21-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacosa-15,19-dien-9-yl]methyl (5Z,8Z,11Z)-icosa-5,8,11-trienoate

> <ALOGPS_LOGP>
4.94

> <JCHEM_LOGP>
8.02796515534421

> <ALOGPS_LOGS>
-4.95

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2719876891721835

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8717053965869859

> <JCHEM_PKA_STRONGEST_BASIC>
0.3666027227537353

> <JCHEM_POLAR_SURFACE_AREA>
300.57

> <JCHEM_REFRACTIVITY>
284.1028

> <JCHEM_ROTATABLE_BOND_COUNT>
25

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.22e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,9R,15Z,18S,22R,23S,24S,26R)-26-(4-amino-2-oxopyrimidin-1-yl)-4,6,23,24-tetrahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,21-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacosa-15,19-dien-9-yl]methyl (5Z,8Z,11Z)-icosa-5,8,11-trienoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0291939 (CDP-DG(20:3(5Z,8Z,11Z)/PGJ2))

HMDB0291939
     RDKit          3D
CDP-DG(20:3(5Z,8Z,11Z)/PGJ2)
155157  0  0  0  0  0  0  0  0999 V2000
   15.9317   -0.6303    4.0206 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9251   -0.7410    2.4774 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2101   -0.2634    1.9344 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5752   -0.3031    0.5333 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8913    0.3331   -0.5814 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6151   -0.0377   -1.1671 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3530   -0.0739   -0.4325 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1638   -0.4080   -1.3707 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9881    0.5515   -2.4454 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9810    1.3271   -2.6901 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7216    1.4932   -1.9786 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4502    0.7742   -0.7535 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4699   -0.1086   -0.5959 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5339   -0.4840   -1.6241 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1347   -0.2167   -1.4413 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5377    0.3892   -0.4702 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0456    1.0013    0.7397 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6050    0.3801    2.0270 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1548    0.2612    2.2774 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4823   -0.7056    1.4079 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1235   -1.6090    0.7847 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0957   -0.6865    1.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5051   -1.6462    0.3758 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0221   -1.4083    0.3094 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3872   -1.3549    1.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3164   -0.0162    2.1141 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1333    0.7175    1.6755 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.6767    1.4026    2.9112 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2114   -0.5020    1.2348 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8356    1.8083    0.4446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1770    2.6852   -0.0440 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.0754    2.8534   -1.5638 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1925    4.2568    0.5965 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5957    1.8608    0.2622 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7320    2.6630    0.0404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9041    1.6626    0.1274 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.8178    0.9094   -1.0212 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9181    0.1825   -1.3698 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.5182    0.5785   -2.6241 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8921    0.2742   -3.7750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4105    0.6143   -5.0065 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6171    1.2944   -5.0994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1825    1.6580   -6.3406 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2212    1.5855   -3.9142 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6861    1.2382   -2.7379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3125    1.5467   -1.6925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6640   -1.3273   -1.3083 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.4757   -2.0081   -0.2918 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1823   -2.3704    0.9234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7999   -1.5603    2.0665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7205   -1.8560    2.6474 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5643   -0.4035    2.6304 C   0  0  2  0  0  0  0  0  0  0  0  0
   -9.0071   -0.6125    2.5851 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9863    0.2022    2.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4486   -0.2920    2.3109 C   0  0  1  0  0  0  0  0  0  0  0  0
  -11.8686   -0.0135    3.6036 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2191    0.3677    1.2347 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6375   -0.0811    1.1730 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3766    0.2072    2.4312 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.8340   -0.2513    2.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.3687    0.5472    1.0540 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0348    0.9097    2.2660 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.8944    1.7875    1.6431 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7892    0.8411    1.3852 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6400    1.2391    2.0594 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1965   -1.6638   -1.2852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7504   -2.5045   -2.4058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5518   -2.4083   -2.9721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7565   -1.1589   -3.0179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7150   -1.0831   -1.9508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3120   -1.2189   -2.5409 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3970   -2.3561   -1.8953 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8964   -3.2325   -2.6731 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4816   -2.4132   -0.5258 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8749   -0.7583    4.3179 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.2646    0.3775    4.2788 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.5563   -1.4437    4.4227 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1463    0.0395    2.2067 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6119   -1.7360    2.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.4022    0.8181    2.3059 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.0201   -0.8545    2.5127 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.7487   -1.4382    0.2732 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.6988    0.0473    0.4892 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.6640    0.4635   -1.4572 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.7516    1.4575   -0.2526 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.5040    0.6396   -2.1012 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.7871   -1.0479   -1.7097 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.1230    0.8445    0.0779 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.3825   -0.9546    0.2851 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2736   -0.6670   -0.8383 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5208   -1.3949   -1.8635 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8366    0.6429   -3.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1123    1.9815   -3.6117 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6428    2.6350   -1.7209 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8790    1.4151   -2.7213 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0827    0.9853    0.1435 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4294   -0.5863    0.4142 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6298   -1.6496   -1.7203 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8657   -0.1835   -2.6667 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4637   -0.5943   -2.2724 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4163    0.4986   -0.6118 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5353    2.0593    0.7806 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1110    1.2129    0.7858 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0894    0.9419    2.8835 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0619   -0.6560    2.1113 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6352    1.2477    2.1939 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0257   -0.0822    3.3415 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6953   -2.6868    0.7389 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9323   -1.6041   -0.6463 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9018   -0.4178   -0.2290 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9802   -1.9656    2.3785 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.9655    4.3593    1.2113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7584    3.1205   -0.9462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8810    3.3605    0.8855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8132    2.2595    0.1533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7158    0.3506   -0.6097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9585   -0.2495   -3.7479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9116    0.3714   -5.9335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9217    1.0618   -6.7552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8591    2.5084   -6.8239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0092   -1.6999   -2.3270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5190   -2.2664   -0.6098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2471   -3.4852    1.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3385   -0.4982    3.7742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4065   -1.6473    2.8571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8202    1.2200    2.0030 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4246   -1.3829    2.1665 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5017   -0.6694    4.2288 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1789    1.4784    1.3904 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7675    0.1608    0.2198 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.1670    0.3240    0.2707 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6645   -1.2067    0.9975 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.9771   -0.4349    3.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3540    1.2632    2.7113 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.3934   -0.1073    3.1524 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.7747   -1.3264    1.9824 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.1750    0.0351    0.0997 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.9044    1.5613    0.9964 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.4779    0.6444    1.2244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6602    1.5024    3.1752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7660    2.7110    1.9018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6481   -0.1998    1.1170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8151    1.5916    2.9626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0143   -2.2278   -0.3411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5628   -0.7546   -1.2096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4678   -3.2531   -2.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1270   -3.2952   -3.4290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2938   -1.0410   -4.0332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4789   -0.3090   -2.9252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8996   -1.8968   -1.2172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7885   -0.0968   -1.4521 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2742   -0.3055   -2.3289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4028   -1.3364   -3.6210 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  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  2  0
 27 29  1  0
 27 30  1  0
 30 31  1  0
 31 32  2  0
 31 33  1  0
 31 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  1  0
 37 38  1  0
 38 39  1  0
 39 40  1  0
 40 41  2  0
 41 42  1  0
 42 43  1  0
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 44 45  1  0
 45 46  2  0
 38 47  1  0
 47 48  1  0
 48 49  2  0
 49 50  1  0
 50 51  2  0
 50 52  1  0
 52 53  1  0
 53 54  2  0
 54 55  1  0
 55 56  1  0
 55 57  1  0
 57 58  1  0
 58 59  1  0
 59 60  1  0
 60 61  1  0
 52 62  1  0
 62 63  1  0
 62 64  1  0
 64 65  1  0
 47 66  1  0
 66 67  1  0
 67 68  2  0
 68 69  1  0
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 70 71  1  0
 71 72  1  0
 72 73  2  0
 72 74  1  0
 74 24  1  0
 64 36  1  0
 45 39  1  0
  1 75  1  0
  1 76  1  0
  1 77  1  0
  2 78  1  0
  2 79  1  0
  3 80  1  0
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  4 82  1  0
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  5 85  1  0
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  6 87  1  0
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  7 89  1  0
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 25112  1  0
 29113  1  0
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 35115  1  0
 35116  1  0
 36117  1  1
 38118  1  1
 40119  1  0
 41120  1  0
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 68149  1  0
 69150  1  0
 69151  1  0
 70152  1  0
 70153  1  0
 71154  1  0
 71155  1  0
M  END
Download

PDB for HMDB0291939 (CDP-DG(20:3(5Z,8Z,11Z)/PGJ2))

HEADER    PROTEIN                                 17-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-21         0                                  
HETATM    1  N   UNK     0      14.691 -16.104   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      13.930 -14.700   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      12.391 -14.647   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      11.667 -13.288   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      10.315 -14.171   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      12.482 -11.982   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      14.021 -12.034   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.745 -13.393   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.758 -10.623   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      10.224 -11.067   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.662 -10.633   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.936  -9.143   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       7.082  -8.798   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       6.044  -7.606   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0       4.923  -8.869   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.389  -7.626   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.950  -6.008   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       6.692  -4.614   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       5.265  -3.616   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.914  -4.726   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.809  -3.464   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       9.181  -2.659   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      10.769  -2.733   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.881  -0.800   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      10.218   0.889   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       9.367   2.349   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       7.846   2.963   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      10.539   3.375   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      10.130   4.895   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      11.577   5.533   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      11.154   7.052   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.511   7.835   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      13.844   7.065   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.844   5.525   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      15.178   4.755   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      16.512   5.525   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      17.845   4.755   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      19.179   5.525   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      19.179   7.065   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      20.513   7.835   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      20.513   9.375   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      21.846  10.145   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      23.180   9.375   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      23.180   7.835   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      24.514   7.065   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      24.514   5.525   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0      12.288  -2.275   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0      13.841  -1.965   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      14.685  -0.608   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0      15.428  -2.011   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      16.273  -3.347   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      16.543  -4.924   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      16.248  -6.504   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      15.491  -7.901   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      14.561  -9.206   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      12.994  -9.588   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      12.735  -8.027   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      12.412  -6.491   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      11.026  -5.750   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      10.409  -4.448   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0       9.713  -6.514   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       9.623  -5.148   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       9.706  -3.552   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0       8.223  -2.316   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0       9.609  -1.464   0.000  0.00  0.00           O+0
HETATM   66  C   UNK     0       6.572  -1.132   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0       4.976  -0.493   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0       3.330  -0.235   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0       2.477   1.046   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0       0.940   0.948   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0       8.008  -9.173   0.000  0.00  0.00           C+0
HETATM   72  O   UNK     0       6.350  -9.953   0.000  0.00  0.00           O+0
HETATM   73  C   UNK     0       8.517  -7.553   0.000  0.00  0.00           C+0
HETATM   74  O   UNK     0       7.199  -6.627   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    2                                                       
CONECT    9    6   10   56                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   71                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14   18                                                       
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   47                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45                                                            
CONECT   47   23   48                                                       
CONECT   48   47   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55    9   57                                                  
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59   62   73                                                  
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65   66                                                  
CONECT   65   64                                                            
CONECT   66   64   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69                                                       
CONECT   69   68   70                                                       
CONECT   70   69                                                            
CONECT   71   11   72   73                                                  
CONECT   72   71                                                            
CONECT   73   71   61   74                                                  
CONECT   74   73                                                            
MASTER        0    0    0    0    0    0    0    0   74    0  152    0
END
Download

3D PDB for HMDB0291939 (CDP-DG(20:3(5Z,8Z,11Z)/PGJ2))

COMPND    HMDB0291939
HETATM    1  C1  UNL     1      15.932  -0.630   4.021  1.00  0.00           C  
HETATM    2  C2  UNL     1      15.925  -0.741   2.477  1.00  0.00           C  
HETATM    3  C3  UNL     1      17.210  -0.263   1.934  1.00  0.00           C  
HETATM    4  C4  UNL     1      17.575  -0.303   0.533  1.00  0.00           C  
HETATM    5  C5  UNL     1      16.891   0.333  -0.581  1.00  0.00           C  
HETATM    6  C6  UNL     1      15.615  -0.038  -1.167  1.00  0.00           C  
HETATM    7  C7  UNL     1      14.353  -0.074  -0.432  1.00  0.00           C  
HETATM    8  C8  UNL     1      13.164  -0.408  -1.371  1.00  0.00           C  
HETATM    9  C9  UNL     1      12.988   0.552  -2.445  1.00  0.00           C  
HETATM   10  C10 UNL     1      11.981   1.327  -2.690  1.00  0.00           C  
HETATM   11  C11 UNL     1      10.722   1.493  -1.979  1.00  0.00           C  
HETATM   12  C12 UNL     1      10.450   0.774  -0.753  1.00  0.00           C  
HETATM   13  C13 UNL     1       9.470  -0.109  -0.596  1.00  0.00           C  
HETATM   14  C14 UNL     1       8.534  -0.484  -1.624  1.00  0.00           C  
HETATM   15  C15 UNL     1       7.135  -0.217  -1.441  1.00  0.00           C  
HETATM   16  C16 UNL     1       6.538   0.389  -0.470  1.00  0.00           C  
HETATM   17  C17 UNL     1       7.046   1.001   0.740  1.00  0.00           C  
HETATM   18  C18 UNL     1       6.605   0.380   2.027  1.00  0.00           C  
HETATM   19  C19 UNL     1       5.155   0.261   2.277  1.00  0.00           C  
HETATM   20  C20 UNL     1       4.482  -0.706   1.408  1.00  0.00           C  
HETATM   21  O1  UNL     1       5.123  -1.609   0.785  1.00  0.00           O  
HETATM   22  O2  UNL     1       3.096  -0.686   1.217  1.00  0.00           O  
HETATM   23  C21 UNL     1       2.505  -1.646   0.376  1.00  0.00           C  
HETATM   24  C22 UNL     1       1.022  -1.408   0.309  1.00  0.00           C  
HETATM   25  C23 UNL     1       0.387  -1.355   1.662  1.00  0.00           C  
HETATM   26  O3  UNL     1       0.316  -0.016   2.114  1.00  0.00           O  
HETATM   27  P1  UNL     1      -1.133   0.717   1.676  1.00  0.00           P  
HETATM   28  O4  UNL     1      -1.677   1.403   2.911  1.00  0.00           O  
HETATM   29  O5  UNL     1      -2.211  -0.502   1.235  1.00  0.00           O  
HETATM   30  O6  UNL     1      -0.836   1.808   0.445  1.00  0.00           O  
HETATM   31  P2  UNL     1      -2.177   2.685  -0.044  1.00  0.00           P  
HETATM   32  O7  UNL     1      -2.075   2.853  -1.564  1.00  0.00           O  
HETATM   33  O8  UNL     1      -2.193   4.257   0.596  1.00  0.00           O  
HETATM   34  O9  UNL     1      -3.596   1.861   0.262  1.00  0.00           O  
HETATM   35  C24 UNL     1      -4.732   2.663   0.040  1.00  0.00           C  
HETATM   36  C25 UNL     1      -5.904   1.663   0.127  1.00  0.00           C  
HETATM   37  O10 UNL     1      -5.818   0.909  -1.021  1.00  0.00           O  
HETATM   38  C26 UNL     1      -6.918   0.183  -1.370  1.00  0.00           C  
HETATM   39  N1  UNL     1      -7.518   0.579  -2.624  1.00  0.00           N  
HETATM   40  C27 UNL     1      -6.892   0.274  -3.775  1.00  0.00           C  
HETATM   41  C28 UNL     1      -7.410   0.614  -5.007  1.00  0.00           C  
HETATM   42  C29 UNL     1      -8.617   1.294  -5.099  1.00  0.00           C  
HETATM   43  N2  UNL     1      -9.182   1.658  -6.341  1.00  0.00           N  
HETATM   44  N3  UNL     1      -9.221   1.585  -3.914  1.00  0.00           N  
HETATM   45  C30 UNL     1      -8.686   1.238  -2.738  1.00  0.00           C  
HETATM   46  O11 UNL     1      -9.313   1.547  -1.692  1.00  0.00           O  
HETATM   47  C31 UNL     1      -6.664  -1.327  -1.308  1.00  0.00           C  
HETATM   48  C32 UNL     1      -7.476  -2.008  -0.292  1.00  0.00           C  
HETATM   49  C33 UNL     1      -7.182  -2.370   0.923  1.00  0.00           C  
HETATM   50  C34 UNL     1      -6.800  -1.560   2.067  1.00  0.00           C  
HETATM   51  O12 UNL     1      -5.721  -1.856   2.647  1.00  0.00           O  
HETATM   52  C35 UNL     1      -7.564  -0.403   2.630  1.00  0.00           C  
HETATM   53  C36 UNL     1      -9.007  -0.613   2.585  1.00  0.00           C  
HETATM   54  C37 UNL     1      -9.986   0.202   2.277  1.00  0.00           C  
HETATM   55  C38 UNL     1     -11.449  -0.292   2.311  1.00  0.00           C  
HETATM   56  O13 UNL     1     -11.869  -0.014   3.604  1.00  0.00           O  
HETATM   57  C39 UNL     1     -12.219   0.368   1.235  1.00  0.00           C  
HETATM   58  C40 UNL     1     -13.637  -0.081   1.173  1.00  0.00           C  
HETATM   59  C41 UNL     1     -14.377   0.207   2.431  1.00  0.00           C  
HETATM   60  C42 UNL     1     -15.834  -0.251   2.213  1.00  0.00           C  
HETATM   61  C43 UNL     1     -16.369   0.547   1.054  1.00  0.00           C  
HETATM   62  C44 UNL     1      -7.035   0.910   2.266  1.00  0.00           C  
HETATM   63  O14 UNL     1      -7.894   1.787   1.643  1.00  0.00           O  
HETATM   64  C45 UNL     1      -5.789   0.841   1.385  1.00  0.00           C  
HETATM   65  O15 UNL     1      -4.640   1.239   2.059  1.00  0.00           O  
HETATM   66  C46 UNL     1      -5.196  -1.664  -1.285  1.00  0.00           C  
HETATM   67  C47 UNL     1      -4.750  -2.505  -2.406  1.00  0.00           C  
HETATM   68  C48 UNL     1      -3.552  -2.408  -2.972  1.00  0.00           C  
HETATM   69  C49 UNL     1      -2.756  -1.159  -3.018  1.00  0.00           C  
HETATM   70  C50 UNL     1      -1.715  -1.083  -1.951  1.00  0.00           C  
HETATM   71  C51 UNL     1      -0.312  -1.219  -2.541  1.00  0.00           C  
HETATM   72  C52 UNL     1       0.397  -2.356  -1.895  1.00  0.00           C  
HETATM   73  O16 UNL     1       0.896  -3.233  -2.673  1.00  0.00           O  
HETATM   74  O17 UNL     1       0.482  -2.413  -0.526  1.00  0.00           O  
HETATM   75  H1  UNL     1      14.875  -0.758   4.318  1.00  0.00           H  
HETATM   76  H2  UNL     1      16.265   0.377   4.279  1.00  0.00           H  
HETATM   77  H3  UNL     1      16.556  -1.444   4.423  1.00  0.00           H  
HETATM   78  H4  UNL     1      15.146   0.040   2.207  1.00  0.00           H  
HETATM   79  H5  UNL     1      15.612  -1.736   2.179  1.00  0.00           H  
HETATM   80  H6  UNL     1      17.402   0.818   2.306  1.00  0.00           H  
HETATM   81  H7  UNL     1      18.020  -0.854   2.513  1.00  0.00           H  
HETATM   82  H8  UNL     1      17.749  -1.438   0.273  1.00  0.00           H  
HETATM   83  H9  UNL     1      18.699   0.047   0.489  1.00  0.00           H  
HETATM   84  H10 UNL     1      17.664   0.463  -1.457  1.00  0.00           H  
HETATM   85  H11 UNL     1      16.752   1.458  -0.253  1.00  0.00           H  
HETATM   86  H12 UNL     1      15.504   0.640  -2.101  1.00  0.00           H  
HETATM   87  H13 UNL     1      15.787  -1.048  -1.710  1.00  0.00           H  
HETATM   88  H14 UNL     1      14.123   0.845   0.078  1.00  0.00           H  
HETATM   89  H15 UNL     1      14.383  -0.955   0.285  1.00  0.00           H  
HETATM   90  H16 UNL     1      12.274  -0.667  -0.838  1.00  0.00           H  
HETATM   91  H17 UNL     1      13.521  -1.395  -1.864  1.00  0.00           H  
HETATM   92  H18 UNL     1      13.837   0.643  -3.187  1.00  0.00           H  
HETATM   93  H19 UNL     1      12.112   1.981  -3.612  1.00  0.00           H  
HETATM   94  H20 UNL     1      10.643   2.635  -1.721  1.00  0.00           H  
HETATM   95  H21 UNL     1       9.879   1.415  -2.721  1.00  0.00           H  
HETATM   96  H22 UNL     1      11.083   0.985   0.144  1.00  0.00           H  
HETATM   97  H23 UNL     1       9.429  -0.586   0.414  1.00  0.00           H  
HETATM   98  H24 UNL     1       8.630  -1.650  -1.720  1.00  0.00           H  
HETATM   99  H25 UNL     1       8.866  -0.184  -2.667  1.00  0.00           H  
HETATM  100  H26 UNL     1       6.464  -0.594  -2.272  1.00  0.00           H  
HETATM  101  H27 UNL     1       5.416   0.499  -0.612  1.00  0.00           H  
HETATM  102  H28 UNL     1       6.535   2.059   0.781  1.00  0.00           H  
HETATM  103  H29 UNL     1       8.111   1.213   0.786  1.00  0.00           H  
HETATM  104  H30 UNL     1       7.089   0.942   2.883  1.00  0.00           H  
HETATM  105  H31 UNL     1       7.062  -0.656   2.111  1.00  0.00           H  
HETATM  106  H32 UNL     1       4.635   1.248   2.194  1.00  0.00           H  
HETATM  107  H33 UNL     1       5.026  -0.082   3.341  1.00  0.00           H  
HETATM  108  H34 UNL     1       2.695  -2.687   0.739  1.00  0.00           H  
HETATM  109  H35 UNL     1       2.932  -1.604  -0.646  1.00  0.00           H  
HETATM  110  H36 UNL     1       0.902  -0.418  -0.229  1.00  0.00           H  
HETATM  111  H37 UNL     1       0.980  -1.966   2.378  1.00  0.00           H  
HETATM  112  H38 UNL     1      -0.631  -1.810   1.636  1.00  0.00           H  
HETATM  113  H39 UNL     1      -2.581  -0.919   2.048  1.00  0.00           H  
HETATM  114  H40 UNL     1      -2.966   4.359   1.211  1.00  0.00           H  
HETATM  115  H41 UNL     1      -4.758   3.121  -0.946  1.00  0.00           H  
HETATM  116  H42 UNL     1      -4.881   3.361   0.886  1.00  0.00           H  
HETATM  117  H43 UNL     1      -6.813   2.260   0.153  1.00  0.00           H  
HETATM  118  H44 UNL     1      -7.716   0.351  -0.610  1.00  0.00           H  
HETATM  119  H45 UNL     1      -5.959  -0.249  -3.748  1.00  0.00           H  
HETATM  120  H46 UNL     1      -6.912   0.371  -5.933  1.00  0.00           H  
HETATM  121  H47 UNL     1      -9.922   1.062  -6.755  1.00  0.00           H  
HETATM  122  H48 UNL     1      -8.859   2.508  -6.824  1.00  0.00           H  
HETATM  123  H49 UNL     1      -7.009  -1.700  -2.327  1.00  0.00           H  
HETATM  124  H50 UNL     1      -8.519  -2.266  -0.610  1.00  0.00           H  
HETATM  125  H51 UNL     1      -7.247  -3.485   1.086  1.00  0.00           H  
HETATM  126  H52 UNL     1      -7.338  -0.498   3.774  1.00  0.00           H  
HETATM  127  H53 UNL     1      -9.407  -1.647   2.857  1.00  0.00           H  
HETATM  128  H54 UNL     1      -9.820   1.220   2.003  1.00  0.00           H  
HETATM  129  H55 UNL     1     -11.425  -1.383   2.166  1.00  0.00           H  
HETATM  130  H56 UNL     1     -11.502  -0.669   4.229  1.00  0.00           H  
HETATM  131  H57 UNL     1     -12.179   1.478   1.390  1.00  0.00           H  
HETATM  132  H58 UNL     1     -11.768   0.161   0.220  1.00  0.00           H  
HETATM  133  H59 UNL     1     -14.167   0.324   0.271  1.00  0.00           H  
HETATM  134  H60 UNL     1     -13.665  -1.207   0.997  1.00  0.00           H  
HETATM  135  H61 UNL     1     -13.977  -0.435   3.264  1.00  0.00           H  
HETATM  136  H62 UNL     1     -14.354   1.263   2.711  1.00  0.00           H  
HETATM  137  H63 UNL     1     -16.393  -0.107   3.152  1.00  0.00           H  
HETATM  138  H64 UNL     1     -15.775  -1.326   1.982  1.00  0.00           H  
HETATM  139  H65 UNL     1     -16.175   0.035   0.100  1.00  0.00           H  
HETATM  140  H66 UNL     1     -15.904   1.561   0.996  1.00  0.00           H  
HETATM  141  H67 UNL     1     -17.478   0.644   1.224  1.00  0.00           H  
HETATM  142  H68 UNL     1      -6.660   1.502   3.175  1.00  0.00           H  
HETATM  143  H69 UNL     1      -7.766   2.711   1.902  1.00  0.00           H  
HETATM  144  H70 UNL     1      -5.648  -0.200   1.117  1.00  0.00           H  
HETATM  145  H71 UNL     1      -4.815   1.592   2.963  1.00  0.00           H  
HETATM  146  H72 UNL     1      -5.014  -2.228  -0.341  1.00  0.00           H  
HETATM  147  H73 UNL     1      -4.563  -0.755  -1.210  1.00  0.00           H  
HETATM  148  H74 UNL     1      -5.468  -3.253  -2.787  1.00  0.00           H  
HETATM  149  H75 UNL     1      -3.127  -3.295  -3.429  1.00  0.00           H  
HETATM  150  H76 UNL     1      -2.294  -1.041  -4.033  1.00  0.00           H  
HETATM  151  H77 UNL     1      -3.479  -0.309  -2.925  1.00  0.00           H  
HETATM  152  H78 UNL     1      -1.900  -1.897  -1.217  1.00  0.00           H  
HETATM  153  H79 UNL     1      -1.788  -0.097  -1.452  1.00  0.00           H  
HETATM  154  H80 UNL     1       0.274  -0.305  -2.329  1.00  0.00           H  
HETATM  155  H81 UNL     1      -0.403  -1.336  -3.621  1.00  0.00           H  
CONECT    1    2   75   76   77
CONECT    2    3   78   79
CONECT    3    4   80   81
CONECT    4    5   82   83
CONECT    5    6   84   85
CONECT    6    7   86   87
CONECT    7    8   88   89
CONECT    8    9   90   91
CONECT    9   10   10   92
CONECT   10   11   93
CONECT   11   12   94   95
CONECT   12   13   13   96
CONECT   13   14   97
CONECT   14   15   98   99
CONECT   15   16   16  100
CONECT   16   17  101
CONECT   17   18  102  103
CONECT   18   19  104  105
CONECT   19   20  106  107
CONECT   20   21   21   22
CONECT   22   23
CONECT   23   24  108  109
CONECT   24   25   74  110
CONECT   25   26  111  112
CONECT   26   27
CONECT   27   28   28   29   30
CONECT   29  113
CONECT   30   31
CONECT   31   32   32   33   34
CONECT   33  114
CONECT   34   35
CONECT   35   36  115  116
CONECT   36   37   64  117
CONECT   37   38
CONECT   38   39   47  118
CONECT   39   40   45
CONECT   40   41   41  119
CONECT   41   42  120
CONECT   42   43   44   44
CONECT   43  121  122
CONECT   44   45
CONECT   45   46   46
CONECT   47   48   66  123
CONECT   48   49   49  124
CONECT   49   50  125
CONECT   50   51   51   52
CONECT   52   53   62  126
CONECT   53   54   54  127
CONECT   54   55  128
CONECT   55   56   57  129
CONECT   56  130
CONECT   57   58  131  132
CONECT   58   59  133  134
CONECT   59   60  135  136
CONECT   60   61  137  138
CONECT   61  139  140  141
CONECT   62   63   64  142
CONECT   63  143
CONECT   64   65  144
CONECT   65  145
CONECT   66   67  146  147
CONECT   67   68   68  148
CONECT   68   69  149
CONECT   69   70  150  151
CONECT   70   71  152  153
CONECT   71   72  154  155
CONECT   72   73   73   74
END
Download

SMILES for HMDB0291939 (CDP-DG(20:3(5Z,8Z,11Z)/PGJ2))

CCCCCCCC\C=C/C\C=C/C\C=C/CCCC(=O)OC[C@@H]1COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@@H](CC=CCCCC(=O)O1)C=CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@H](O)[C@@H]2O)N1C=CC(N)=NC1=O
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INCHI for HMDB0291939 (CDP-DG(20:3(5Z,8Z,11Z)/PGJ2))

InChI=1S/C52H81N3O17P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-19-20-25-29-47(58)67-37-42-38-68-73(63,64)72-74(65,66)69-39-45-50(61)49(60)43(33-32-41(56)28-23-6-4-2)44(57)34-31-40(27-24-21-22-26-30-48(59)70-42)51(71-45)55-36-35-46(53)54-52(55)62/h12-13,15-16,18-19,21,24,31-36,40-43,45,49-51,56,60-61H,3-11,14,17,20,22-23,25-30,37-39H2,1-2H3,(H,63,64)(H,65,66)(H2,53,54,62)/b13-12-,16-15-,19-18-,24-21-,33-32+,34-31?/t40-,41?,42+,43-,45+,49-,50+,51+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[(1R,9R,15Z,18S,22R,23S,24S,26R)-4,6,23,24-Tetrahydroxy-26-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-22-(3-hydroxyoct-1-en-1-yl)-4,6,11,21-tetraoxo-3,5,7,10,25-pentaoxa-4,6-diphosphabicyclo[16.6.2]hexacosa-15,19-dien-9-yl]methyl (5Z,8Z,11Z)-icosa-5,8,11-trienoic acidGenerator
Chemical FormulaC52H81N3O17P2
Average Molecular Weight1082.172
Monoisotopic Molecular Weight1081.504122156
IUPAC Name[(1R,9R,15Z,18S,22R,23S,24S,26R)-26-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,23,24-tetrahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,21-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacosa-15,19-dien-9-yl]methyl (5Z,8Z,11Z)-icosa-5,8,11-trienoate
Traditional Name[(1R,9R,15Z,18S,22R,23S,24S,26R)-26-(4-amino-2-oxopyrimidin-1-yl)-4,6,23,24-tetrahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,21-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacosa-15,19-dien-9-yl]methyl (5Z,8Z,11Z)-icosa-5,8,11-trienoate
CAS Registry NumberNot Available
SMILES
CCCCCCCC\C=C/C\C=C/C\C=C/CCCC(=O)OC[C@@H]1COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@@H](CC=CCCCC(=O)O1)C=CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@H](O)[C@@H]2O)N1C=CC(N)=NC1=O
InChI Identifier
InChI=1S/C52H81N3O17P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-19-20-25-29-47(58)67-37-42-38-68-73(63,64)72-74(65,66)69-39-45-50(61)49(60)43(33-32-41(56)28-23-6-4-2)44(57)34-31-40(27-24-21-22-26-30-48(59)70-42)51(71-45)55-36-35-46(53)54-52(55)62/h12-13,15-16,18-19,21,24,31-36,40-43,45,49-51,56,60-61H,3-11,14,17,20,22-23,25-30,37-39H2,1-2H3,(H,63,64)(H,65,66)(H2,53,54,62)/b13-12-,16-15-,19-18-,24-21-,33-32+,34-31?/t40-,41?,42+,43-,45+,49-,50+,51+/m0/s1
InChI KeyPQLKYSWBDHQISO-IVMRCEIQSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP4.94ALOGPS
logP8.03ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)0.37ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area300.57 ŲChemAxon
Rotatable Bond Count25ChemAxon
Refractivity284.1 m³·mol⁻¹ChemAxon
Polarizability115.72 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+316.02432859911
AllCCS[M+H-H2O]+316.5532859911
AllCCS[M+Na]+315.34632859911
AllCCS[M+NH4]+315.50232859911
AllCCS[M-H]-295.62632859911
AllCCS[M+Na-2H]-302.18232859911
AllCCS[M+HCOO]-309.27332859911
DeepCCS[M+H]+304.77930932474
DeepCCS[M-H]-303.05630932474
DeepCCS[M-2H]-337.08730932474
DeepCCS[M+Na]+311.10830932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:3(5Z,8Z,11Z)/PGJ2) 10V, Positive-QTOFsplash10-03e9-9300000003-b6f118d8837cd6ccfc322021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:3(5Z,8Z,11Z)/PGJ2) 20V, Positive-QTOFsplash10-0601-9200000007-fcecf319846674ccc6782021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:3(5Z,8Z,11Z)/PGJ2) 40V, Positive-QTOFsplash10-01t9-5900002701-2d69a8e81b87129ee48b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:3(5Z,8Z,11Z)/PGJ2) 10V, Negative-QTOFsplash10-001i-9000000000-4b899fd845a182549b6b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:3(5Z,8Z,11Z)/PGJ2) 20V, Negative-QTOFsplash10-08gi-9302000401-5f7415cde8da9ab57a762021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:3(5Z,8Z,11Z)/PGJ2) 40V, Negative-QTOFsplash10-00di-7371000900-11f0e1fc54bce429e7542021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]