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Showing metabocard for CDP-DG(PGD2/18:3(6Z,9Z,12Z)) (HMDB0291518)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 00:28:52 UTC
Update Date2022-11-30 20:07:38 UTC
HMDB IDHMDB0291518
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(PGD2/18:3(6Z,9Z,12Z))
DescriptionCDP-DG(PGD2/18:3(6Z,9Z,12Z)) 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(PGD2/18:3(6Z,9Z,12Z)), in particular, consists of one chain of one Prostaglandin D2 at the C-1 position and one chain of 6Z,9Z,12Z-octadecatrienoyl 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 HMDB0291518 (CDP-DG(PGD2/18:3(6Z,9Z,12Z)))


  Mrv1652309172102292D          

 73 75  0  0  1  0            999 V2000
   -5.6710    6.7386    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.7320    5.6760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0291518 (CDP-DG(PGD2/18:3(6Z,9Z,12Z)))

HMDB0291518
     RDKit          3D
CDP-DG(PGD2/18:3(6Z,9Z,12Z))
152154  0  0  0  0  0  0  0  0999 V2000
   14.8668    1.3741   -3.1710 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7744    1.7045   -2.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8296    0.6893   -1.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9477    0.8171    0.1291 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4954    0.7646   -0.0343 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7775    1.7700   -0.8105 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8790    2.5451   -0.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.0894    2.1805    1.3277 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0291518 (CDP-DG(PGD2/18:3(6Z,9Z,12Z)))


  Mrv1652309172102292D          

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 40 72  1  0  0  0  0
 72 73  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0291518

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC\C=C/C\C=C/C\C=C/CCCCC(=O)O[C@@H]1COC(=O)CCC\C=C/C[C@H]2[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@H](O)[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OC1)O[C@H]2N1C=CC(N)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C50H79N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-24-28-46(58)69-38-34-66-45(57)27-23-20-19-22-26-40-42(56)33-41(55)39(30-29-37(54)25-21-6-4-2)47(59)48(60)43(36-68-73(64,65)71-72(62,63)67-35-38)70-49(40)53-32-31-44(51)52-50(53)61/h9-10,12-13,15-16,19,22,29-32,37-40,42-43,47-49,54,56,59-60H,3-8,11,14,17-18,20-21,23-28,33-36H2,1-2H3,(H,62,63)(H,64,65)(H2,51,52,61)/b10-9-,13-12-,16-15-,22-19-,30-29+/t37-,38+,39-,40-,42-,43+,47-,48?,49+/m0/s1

> <INCHI_KEY>
DMEIAHFPIHHNAG-QJEJVIEYSA-N

> <FORMULA>
C50H79N3O18P2

> <MOLECULAR_WEIGHT>
1072.133

> <EXACT_MASS>
1071.483386712

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
152

> <JCHEM_AVERAGE_POLARIZABILITY>
110.62456643248177

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,9R,16Z,19S,20S,23R,24S,25S,27R)-27-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,20,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (6Z,9Z,12Z)-octadeca-6,9,12-trienoate

> <ALOGPS_LOGP>
3.77

> <JCHEM_LOGP>
6.175708731405346

> <ALOGPS_LOGS>
-4.27

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.271952704077896

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8709321252782676

> <JCHEM_PKA_STRONGEST_BASIC>
0.34389111225974733

> <JCHEM_POLAR_SURFACE_AREA>
320.8

> <JCHEM_REFRACTIVITY>
274.9622

> <JCHEM_ROTATABLE_BOND_COUNT>
22

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.70e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,9R,16Z,19S,20S,23R,24S,25S,27R)-27-(4-amino-2-oxopyrimidin-1-yl)-4,6,20,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (6Z,9Z,12Z)-octadeca-6,9,12-trienoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0291518 (CDP-DG(PGD2/18:3(6Z,9Z,12Z)))

HMDB0291518
     RDKit          3D
CDP-DG(PGD2/18:3(6Z,9Z,12Z))
152154  0  0  0  0  0  0  0  0999 V2000
   14.8668    1.3741   -3.1710 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7744    1.7045   -2.1015 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8296    0.6893   -1.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9477    0.8171    0.1291 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4954    0.7646   -0.0343 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7775    1.7700   -0.8105 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8790    2.5451   -0.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5084    2.5058    1.2130 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0894    2.1805    1.3277 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6072    1.1363    1.9673 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4211    0.1714    2.6460 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5127   -1.2237    2.2826 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9492   -1.9333    1.3800 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9693   -1.5184    0.3881 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7819   -2.4450    0.4598 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1180   -2.5182    1.7583 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.6981    0.3323   -0.6624 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0571   -0.0360   -2.1041 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2526   -1.3752   -2.3338 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4552   -2.4228   -2.6036 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3351   -2.9528   -3.7499 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6371   -3.0506   -1.5405 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3084   -2.4181   -1.3155 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8410   -3.3585   -1.5839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3041   -4.0976   -0.3862 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4912   -2.2154    0.4881 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8492   -1.7970    1.0086 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6072   -1.1061    2.2868 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7254   -0.0269    2.0166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6744   -0.7792    3.2173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0583   -0.7930    2.8180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6505   -1.8672    2.7452 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8832    0.4293    2.4688 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.0756    0.0045    1.7322 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2912    0.0978    2.2651 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4727   -0.3351    1.5071 C   0  0  1  0  0  0  0  0  0  0  0  0
  -11.2457   -1.2618    2.2460 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4015    0.7613    1.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7893    1.8049    0.2129 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8677    2.8299   -0.1162 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2394    3.8753   -1.0095 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0786    4.5634   -0.3208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0796    1.5289    1.8758 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4281    2.7042    2.6163 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1621    1.7648    0.4193 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.4511    1.5506   -0.1359 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0711    1.2855   -0.4460 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1124    2.4695   -0.6940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8892    2.2550   -0.0616 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5967    2.1415   -1.1194 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.0357    0.7255   -1.1891 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0505    2.5684   -2.6950 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3054    3.1106   -0.6005 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4522    2.3194    0.6860 P   0  0  0  0  0  5  0  0  0  0  0  0
    0.0028    3.0278    1.9488 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0262    0.7219    0.8128 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1357    2.3389    0.5721 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5909    1.8625   -0.6364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2993    0.2548   -0.1812 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6416   -1.0090   -0.0400 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7066   -1.8589   -1.2081 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2989   -3.0623   -1.1702 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4005   -3.9148   -2.2425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8572   -3.5127   -3.4476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9172   -4.3275   -4.6099 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2597   -2.2948   -3.4786 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1882   -1.4875   -2.3782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6272   -0.3816   -2.4691 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7444    0.9180   -2.6570 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.4812    0.6085   -3.8755 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1135    2.2897   -3.7424 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.8303    1.6319   -2.6650 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.9958    2.7353   -1.7656 H   0  0  0  0  0  0  0  0  0  0  0  0
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   14.9195    0.6318   -0.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2732    1.7241    0.7481 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2187   -0.0228    0.8754 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3018   -0.2215   -0.6273 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9559    0.5070    0.9273 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8787    1.9498   -1.8834 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3468    3.2958   -0.8227 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5722    3.6235    1.5471 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2096    2.0345    1.8851 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3742    2.8573    0.8443 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4900    1.0566    1.9965 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.8755    5.5593   -0.8116 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2657    4.7812    0.7344 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0028    1.4161    2.1345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1193    3.2172    2.1361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1278    2.9106    0.3271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2742    1.1486   -1.0166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5731    1.1701   -1.4648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5711    3.4237   -0.3600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8738    2.5823   -1.7721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1930    1.8129   -3.2894 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1155    0.4226    1.7474 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5928    2.3172   -0.8083 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9205    2.2237   -1.4495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6958   -1.0627    0.3400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7441   -3.4185   -0.2286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8818   -4.8851   -2.1999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3042   -5.1468   -4.7010 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5805   -4.0889   -5.3596 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  2  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  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  2  0
 24 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  2  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 33 35  1  0
 35 36  1  0
 36 37  2  0
 36 38  1  0
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 39 40  2  0
 40 41  1  0
 41 42  1  0
 41 43  1  0
 43 44  1  0
 44 45  1  0
 45 46  1  0
 46 47  1  0
 38 48  1  0
 48 49  1  0
 48 50  1  0
 50 51  1  0
 50 52  1  0
 52 53  1  0
 53 54  1  0
 54 55  1  0
 55 56  2  0
 55 57  1  0
 55 58  1  0
 58 59  1  0
 59 60  2  0
 59 61  1  0
 59 62  1  0
 62 63  1  0
 52 64  1  0
 64 65  1  0
 65 66  1  0
 66 67  1  0
 67 68  2  0
 68 69  1  0
 69 70  1  0
 69 71  2  0
 71 72  1  0
 72 73  2  0
 63 21  1  0
 72 66  1  0
 65 32  1  0
  1 74  1  0
  1 75  1  0
  1 76  1  0
  2 77  1  0
  2 78  1  0
  3 79  1  0
  3 80  1  0
  4 81  1  0
  4 82  1  0
  5 83  1  0
  5 84  1  0
  6 85  1  0
  7 86  1  0
  8 87  1  0
  8 88  1  0
  9 89  1  0
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 14 96  1  0
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 16 99  1  0
 16100  1  0
 17101  1  0
 17102  1  0
 21103  1  1
 22104  1  0
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 26106  1  0
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 28110  1  0
 28111  1  0
 29112  1  0
 30113  1  0
 31114  1  0
 31115  1  0
 32116  1  1
 33117  1  1
 34118  1  0
 35119  1  0
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 48137  1  6
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 50139  1  1
 51140  1  0
 52141  1  6
 53142  1  0
 53143  1  0
 57144  1  0
 61145  1  0
 63146  1  0
 63147  1  0
 65148  1  1
 67149  1  0
 68150  1  0
 70151  1  0
 70152  1  0
M  END
Download

PDB for HMDB0291518 (CDP-DG(PGD2/18:3(6Z,9Z,12Z)))

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     -10.586  12.579   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -9.004  12.316   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -8.011  13.493   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -6.495  13.221   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -6.647  14.840   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -5.973  11.772   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -6.966  10.595   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -8.482  10.867   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.457  11.500   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.932  12.993   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.932  14.222   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.318  15.684   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.013  16.582   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       0.585  16.629   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0      -0.287  18.048   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.154  18.180   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.017  15.923   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       3.129  14.774   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       3.624  16.333   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.807  15.464   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       3.788  13.318   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.008  11.750   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.722  10.183   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.127   8.707   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.148   7.465   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       0.967   6.436   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.753   4.991   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -0.355   5.599   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.796   4.973   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.373   4.853   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.771   5.573   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.456   6.981   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.287   8.531   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.484   9.904   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -2.994   9.421   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -3.480   7.980   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -1.442   9.297   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -0.147  10.175   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -0.205   8.633   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       0.473  11.599   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       2.041  11.558   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       3.359  12.495   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       5.230  12.993   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0       6.205  14.458   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       6.905  12.860   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       8.494  13.132   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       9.380  11.853   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      10.871  11.491   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      11.304  10.013   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0       5.160   9.017   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0       6.375   7.696   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0       6.450   6.112   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0       7.978   6.974   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       9.705   7.074   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      11.374   6.882   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      12.832   7.696   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      14.457   7.946   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      15.490   9.186   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      14.958  10.632   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      13.440  10.893   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      12.908  12.339   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      13.894  13.522   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      15.412  13.260   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      16.397  14.443   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      15.865  15.889   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      16.851  17.072   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      16.319  18.517   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      17.304  19.700   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      16.772  21.146   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      -1.513  13.583   0.000  0.00  0.00           C+0
HETATM   71  O   UNK     0      -1.256  12.121   0.000  0.00  0.00           O+0
HETATM   72  C   UNK     0      -0.079  13.040   0.000  0.00  0.00           C+0
HETATM   73  O   UNK     0      -0.422  14.554   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   34                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   70                                                  
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   50                                                  
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    9   35                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41   72                                                  
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48                                                            
CONECT   50   23   51                                                       
CONECT   51   50   52   53                                                  
CONECT   52   51                                                            
CONECT   53   51   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   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                                                            
CONECT   70   11   71   72                                                  
CONECT   71   70                                                            
CONECT   72   70   40   73                                                  
CONECT   73   72                                                            
MASTER        0    0    0    0    0    0    0    0   73    0  150    0
END
Download

3D PDB for HMDB0291518 (CDP-DG(PGD2/18:3(6Z,9Z,12Z)))

COMPND    HMDB0291518
HETATM    1  C1  UNL     1      14.867   1.374  -3.171  1.00  0.00           C  
HETATM    2  C2  UNL     1      13.774   1.705  -2.102  1.00  0.00           C  
HETATM    3  C3  UNL     1      13.830   0.689  -1.022  1.00  0.00           C  
HETATM    4  C4  UNL     1      12.948   0.817   0.129  1.00  0.00           C  
HETATM    5  C5  UNL     1      11.495   0.765  -0.034  1.00  0.00           C  
HETATM    6  C6  UNL     1      10.778   1.770  -0.810  1.00  0.00           C  
HETATM    7  C7  UNL     1       9.879   2.545  -0.213  1.00  0.00           C  
HETATM    8  C8  UNL     1       9.508   2.506   1.213  1.00  0.00           C  
HETATM    9  C9  UNL     1       8.089   2.180   1.328  1.00  0.00           C  
HETATM   10  C10 UNL     1       7.607   1.136   1.967  1.00  0.00           C  
HETATM   11  C11 UNL     1       8.421   0.171   2.646  1.00  0.00           C  
HETATM   12  C12 UNL     1       8.513  -1.224   2.283  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.949  -1.933   1.380  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.969  -1.518   0.388  1.00  0.00           C  
HETATM   15  C15 UNL     1       5.782  -2.445   0.460  1.00  0.00           C  
HETATM   16  C16 UNL     1       5.118  -2.518   1.758  1.00  0.00           C  
HETATM   17  C17 UNL     1       4.478  -1.271   2.298  1.00  0.00           C  
HETATM   18  C18 UNL     1       3.472  -0.834   1.302  1.00  0.00           C  
HETATM   19  O1  UNL     1       2.287  -1.233   1.435  1.00  0.00           O  
HETATM   20  O2  UNL     1       3.747  -0.008   0.221  1.00  0.00           O  
HETATM   21  C19 UNL     1       2.698   0.332  -0.662  1.00  0.00           C  
HETATM   22  C20 UNL     1       3.057  -0.036  -2.104  1.00  0.00           C  
HETATM   23  O3  UNL     1       3.253  -1.375  -2.334  1.00  0.00           O  
HETATM   24  C21 UNL     1       2.455  -2.423  -2.604  1.00  0.00           C  
HETATM   25  O4  UNL     1       2.335  -2.953  -3.750  1.00  0.00           O  
HETATM   26  C22 UNL     1       1.637  -3.051  -1.540  1.00  0.00           C  
HETATM   27  C23 UNL     1       0.308  -2.418  -1.316  1.00  0.00           C  
HETATM   28  C24 UNL     1      -0.841  -3.359  -1.584  1.00  0.00           C  
HETATM   29  C25 UNL     1      -1.304  -4.098  -0.386  1.00  0.00           C  
HETATM   30  C26 UNL     1      -2.258  -3.639   0.409  1.00  0.00           C  
HETATM   31  C27 UNL     1      -2.491  -2.215   0.488  1.00  0.00           C  
HETATM   32  C28 UNL     1      -3.849  -1.797   1.009  1.00  0.00           C  
HETATM   33  C29 UNL     1      -3.607  -1.106   2.287  1.00  0.00           C  
HETATM   34  O5  UNL     1      -2.725  -0.027   2.017  1.00  0.00           O  
HETATM   35  C30 UNL     1      -4.674  -0.779   3.217  1.00  0.00           C  
HETATM   36  C31 UNL     1      -6.058  -0.793   2.818  1.00  0.00           C  
HETATM   37  O6  UNL     1      -6.651  -1.867   2.745  1.00  0.00           O  
HETATM   38  C32 UNL     1      -6.883   0.429   2.469  1.00  0.00           C  
HETATM   39  C33 UNL     1      -8.076   0.004   1.732  1.00  0.00           C  
HETATM   40  C34 UNL     1      -9.291   0.098   2.265  1.00  0.00           C  
HETATM   41  C35 UNL     1     -10.473  -0.335   1.507  1.00  0.00           C  
HETATM   42  O7  UNL     1     -11.246  -1.262   2.246  1.00  0.00           O  
HETATM   43  C36 UNL     1     -11.402   0.761   1.092  1.00  0.00           C  
HETATM   44  C37 UNL     1     -10.789   1.805   0.213  1.00  0.00           C  
HETATM   45  C38 UNL     1     -11.868   2.830  -0.116  1.00  0.00           C  
HETATM   46  C39 UNL     1     -11.239   3.875  -1.010  1.00  0.00           C  
HETATM   47  C40 UNL     1     -10.079   4.563  -0.321  1.00  0.00           C  
HETATM   48  C41 UNL     1      -6.080   1.529   1.876  1.00  0.00           C  
HETATM   49  O8  UNL     1      -6.428   2.704   2.616  1.00  0.00           O  
HETATM   50  C42 UNL     1      -6.162   1.765   0.419  1.00  0.00           C  
HETATM   51  O9  UNL     1      -7.451   1.551  -0.136  1.00  0.00           O  
HETATM   52  C43 UNL     1      -5.071   1.286  -0.446  1.00  0.00           C  
HETATM   53  C44 UNL     1      -4.112   2.469  -0.694  1.00  0.00           C  
HETATM   54  O10 UNL     1      -2.889   2.255  -0.062  1.00  0.00           O  
HETATM   55  P1  UNL     1      -1.597   2.142  -1.119  1.00  0.00           P  
HETATM   56  O11 UNL     1      -1.036   0.726  -1.189  1.00  0.00           O  
HETATM   57  O12 UNL     1      -2.051   2.568  -2.695  1.00  0.00           O  
HETATM   58  O13 UNL     1      -0.305   3.111  -0.600  1.00  0.00           O  
HETATM   59  P2  UNL     1       0.452   2.319   0.686  1.00  0.00           P  
HETATM   60  O14 UNL     1       0.003   3.028   1.949  1.00  0.00           O  
HETATM   61  O15 UNL     1      -0.026   0.722   0.813  1.00  0.00           O  
HETATM   62  O16 UNL     1       2.136   2.339   0.572  1.00  0.00           O  
HETATM   63  C45 UNL     1       2.591   1.863  -0.636  1.00  0.00           C  
HETATM   64  O17 UNL     1      -4.299   0.255  -0.181  1.00  0.00           O  
HETATM   65  C46 UNL     1      -4.642  -1.009  -0.040  1.00  0.00           C  
HETATM   66  N1  UNL     1      -4.707  -1.859  -1.208  1.00  0.00           N  
HETATM   67  C47 UNL     1      -5.299  -3.062  -1.170  1.00  0.00           C  
HETATM   68  C48 UNL     1      -5.400  -3.915  -2.243  1.00  0.00           C  
HETATM   69  C49 UNL     1      -4.857  -3.513  -3.448  1.00  0.00           C  
HETATM   70  N2  UNL     1      -4.917  -4.328  -4.610  1.00  0.00           N  
HETATM   71  N3  UNL     1      -4.260  -2.295  -3.479  1.00  0.00           N  
HETATM   72  C50 UNL     1      -4.188  -1.488  -2.378  1.00  0.00           C  
HETATM   73  O18 UNL     1      -3.627  -0.382  -2.469  1.00  0.00           O  
HETATM   74  H1  UNL     1      15.744   0.918  -2.657  1.00  0.00           H  
HETATM   75  H2  UNL     1      14.481   0.608  -3.876  1.00  0.00           H  
HETATM   76  H3  UNL     1      15.113   2.290  -3.742  1.00  0.00           H  
HETATM   77  H4  UNL     1      12.830   1.632  -2.665  1.00  0.00           H  
HETATM   78  H5  UNL     1      13.996   2.735  -1.766  1.00  0.00           H  
HETATM   79  H6  UNL     1      13.681  -0.328  -1.516  1.00  0.00           H  
HETATM   80  H7  UNL     1      14.920   0.632  -0.673  1.00  0.00           H  
HETATM   81  H8  UNL     1      13.273   1.724   0.748  1.00  0.00           H  
HETATM   82  H9  UNL     1      13.219  -0.023   0.875  1.00  0.00           H  
HETATM   83  H10 UNL     1      11.302  -0.222  -0.627  1.00  0.00           H  
HETATM   84  H11 UNL     1      10.956   0.507   0.927  1.00  0.00           H  
HETATM   85  H12 UNL     1      10.879   1.950  -1.883  1.00  0.00           H  
HETATM   86  H13 UNL     1       9.347   3.296  -0.823  1.00  0.00           H  
HETATM   87  H14 UNL     1       9.572   3.623   1.547  1.00  0.00           H  
HETATM   88  H15 UNL     1      10.210   2.035   1.885  1.00  0.00           H  
HETATM   89  H16 UNL     1       7.374   2.857   0.844  1.00  0.00           H  
HETATM   90  H17 UNL     1       6.490   1.057   1.997  1.00  0.00           H  
HETATM   91  H18 UNL     1       9.466   0.577   2.778  1.00  0.00           H  
HETATM   92  H19 UNL     1       8.090   0.169   3.771  1.00  0.00           H  
HETATM   93  H20 UNL     1       9.248  -1.823   2.945  1.00  0.00           H  
HETATM   94  H21 UNL     1       8.229  -3.015   1.326  1.00  0.00           H  
HETATM   95  H22 UNL     1       6.587  -0.503   0.423  1.00  0.00           H  
HETATM   96  H23 UNL     1       7.470  -1.663  -0.627  1.00  0.00           H  
HETATM   97  H24 UNL     1       5.054  -2.091  -0.322  1.00  0.00           H  
HETATM   98  H25 UNL     1       6.100  -3.462   0.104  1.00  0.00           H  
HETATM   99  H26 UNL     1       5.814  -2.975   2.523  1.00  0.00           H  
HETATM  100  H27 UNL     1       4.276  -3.278   1.697  1.00  0.00           H  
HETATM  101  H28 UNL     1       3.878  -1.648   3.207  1.00  0.00           H  
HETATM  102  H29 UNL     1       5.148  -0.515   2.655  1.00  0.00           H  
HETATM  103  H30 UNL     1       1.774  -0.140  -0.339  1.00  0.00           H  
HETATM  104  H31 UNL     1       4.069   0.463  -2.250  1.00  0.00           H  
HETATM  105  H32 UNL     1       2.400   0.516  -2.799  1.00  0.00           H  
HETATM  106  H33 UNL     1       2.273  -3.032  -0.618  1.00  0.00           H  
HETATM  107  H34 UNL     1       1.447  -4.128  -1.749  1.00  0.00           H  
HETATM  108  H35 UNL     1       0.215  -1.572  -2.010  1.00  0.00           H  
HETATM  109  H36 UNL     1       0.287  -2.009  -0.284  1.00  0.00           H  
HETATM  110  H37 UNL     1      -1.649  -2.823  -2.104  1.00  0.00           H  
HETATM  111  H38 UNL     1      -0.458  -4.099  -2.346  1.00  0.00           H  
HETATM  112  H39 UNL     1      -0.807  -5.065  -0.188  1.00  0.00           H  
HETATM  113  H40 UNL     1      -2.830  -4.347   0.972  1.00  0.00           H  
HETATM  114  H41 UNL     1      -1.725  -1.761   1.152  1.00  0.00           H  
HETATM  115  H42 UNL     1      -2.309  -1.680  -0.496  1.00  0.00           H  
HETATM  116  H43 UNL     1      -4.400  -2.746   1.239  1.00  0.00           H  
HETATM  117  H44 UNL     1      -2.891  -1.803   2.851  1.00  0.00           H  
HETATM  118  H45 UNL     1      -2.781   0.628   2.768  1.00  0.00           H  
HETATM  119  H46 UNL     1      -4.626  -1.417   4.167  1.00  0.00           H  
HETATM  120  H47 UNL     1      -4.446   0.244   3.659  1.00  0.00           H  
HETATM  121  H48 UNL     1      -7.253   0.758   3.497  1.00  0.00           H  
HETATM  122  H49 UNL     1      -8.035  -0.423   0.729  1.00  0.00           H  
HETATM  123  H50 UNL     1      -9.430   0.500   3.281  1.00  0.00           H  
HETATM  124  H51 UNL     1     -10.159  -0.880   0.580  1.00  0.00           H  
HETATM  125  H52 UNL     1     -11.662  -1.927   1.673  1.00  0.00           H  
HETATM  126  H53 UNL     1     -12.216   0.263   0.490  1.00  0.00           H  
HETATM  127  H54 UNL     1     -11.930   1.205   1.976  1.00  0.00           H  
HETATM  128  H55 UNL     1      -9.928   2.316   0.707  1.00  0.00           H  
HETATM  129  H56 UNL     1     -10.461   1.333  -0.717  1.00  0.00           H  
HETATM  130  H57 UNL     1     -12.694   2.375  -0.686  1.00  0.00           H  
HETATM  131  H58 UNL     1     -12.293   3.297   0.789  1.00  0.00           H  
HETATM  132  H59 UNL     1     -10.855   3.343  -1.926  1.00  0.00           H  
HETATM  133  H60 UNL     1     -11.976   4.609  -1.387  1.00  0.00           H  
HETATM  134  H61 UNL     1      -9.169   3.934  -0.374  1.00  0.00           H  
HETATM  135  H62 UNL     1      -9.875   5.559  -0.812  1.00  0.00           H  
HETATM  136  H63 UNL     1     -10.266   4.781   0.734  1.00  0.00           H  
HETATM  137  H64 UNL     1      -5.003   1.416   2.134  1.00  0.00           H  
HETATM  138  H65 UNL     1      -7.119   3.217   2.136  1.00  0.00           H  
HETATM  139  H66 UNL     1      -6.128   2.911   0.327  1.00  0.00           H  
HETATM  140  H67 UNL     1      -7.274   1.149  -1.017  1.00  0.00           H  
HETATM  141  H68 UNL     1      -5.573   1.170  -1.465  1.00  0.00           H  
HETATM  142  H69 UNL     1      -4.571   3.424  -0.360  1.00  0.00           H  
HETATM  143  H70 UNL     1      -3.874   2.582  -1.772  1.00  0.00           H  
HETATM  144  H71 UNL     1      -2.193   1.813  -3.289  1.00  0.00           H  
HETATM  145  H72 UNL     1       0.115   0.423   1.747  1.00  0.00           H  
HETATM  146  H73 UNL     1       3.593   2.317  -0.808  1.00  0.00           H  
HETATM  147  H74 UNL     1       1.920   2.224  -1.449  1.00  0.00           H  
HETATM  148  H75 UNL     1      -5.696  -1.063   0.340  1.00  0.00           H  
HETATM  149  H76 UNL     1      -5.744  -3.418  -0.229  1.00  0.00           H  
HETATM  150  H77 UNL     1      -5.882  -4.885  -2.200  1.00  0.00           H  
HETATM  151  H78 UNL     1      -4.304  -5.147  -4.701  1.00  0.00           H  
HETATM  152  H79 UNL     1      -5.581  -4.089  -5.360  1.00  0.00           H  
CONECT    1    2   74   75   76
CONECT    2    3   77   78
CONECT    3    4   79   80
CONECT    4    5   81   82
CONECT    5    6   83   84
CONECT    6    7    7   85
CONECT    7    8   86
CONECT    8    9   87   88
CONECT    9   10   10   89
CONECT   10   11   90
CONECT   11   12   91   92
CONECT   12   13   13   93
CONECT   13   14   94
CONECT   14   15   95   96
CONECT   15   16   97   98
CONECT   16   17   99  100
CONECT   17   18  101  102
CONECT   18   19   19   20
CONECT   20   21
CONECT   21   22   63  103
CONECT   22   23  104  105
CONECT   23   24
CONECT   24   25   25   26
CONECT   26   27  106  107
CONECT   27   28  108  109
CONECT   28   29  110  111
CONECT   29   30   30  112
CONECT   30   31  113
CONECT   31   32  114  115
CONECT   32   33   65  116
CONECT   33   34   35  117
CONECT   34  118
CONECT   35   36  119  120
CONECT   36   37   37   38
CONECT   38   39   48  121
CONECT   39   40   40  122
CONECT   40   41  123
CONECT   41   42   43  124
CONECT   42  125
CONECT   43   44  126  127
CONECT   44   45  128  129
CONECT   45   46  130  131
CONECT   46   47  132  133
CONECT   47  134  135  136
CONECT   48   49   50  137
CONECT   49  138
CONECT   50   51   52  139
CONECT   51  140
CONECT   52   53   64  141
CONECT   53   54  142  143
CONECT   54   55
CONECT   55   56   56   57   58
CONECT   57  144
CONECT   58   59
CONECT   59   60   60   61   62
CONECT   61  145
CONECT   62   63
CONECT   63  146  147
CONECT   64   65
CONECT   65   66  148
CONECT   66   67   72
CONECT   67   68   68  149
CONECT   68   69  150
CONECT   69   70   71   71
CONECT   70  151  152
CONECT   71   72
CONECT   72   73   73
END
Download

SMILES for HMDB0291518 (CDP-DG(PGD2/18:3(6Z,9Z,12Z)))

CCCCC\C=C/C\C=C/C\C=C/CCCCC(=O)O[C@@H]1COC(=O)CCC\C=C/C[C@H]2[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@H](O)[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OC1)O[C@H]2N1C=CC(N)=NC1=O
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INCHI for HMDB0291518 (CDP-DG(PGD2/18:3(6Z,9Z,12Z)))

InChI=1S/C50H79N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-24-28-46(58)69-38-34-66-45(57)27-23-20-19-22-26-40-42(56)33-41(55)39(30-29-37(54)25-21-6-4-2)47(59)48(60)43(36-68-73(64,65)71-72(62,63)67-35-38)70-49(40)53-32-31-44(51)52-50(53)61/h9-10,12-13,15-16,19,22,29-32,37-40,42-43,47-49,54,56,59-60H,3-8,11,14,17-18,20-21,23-28,33-36H2,1-2H3,(H,62,63)(H,64,65)(H2,51,52,61)/b10-9-,13-12-,16-15-,22-19-,30-29+/t37-,38+,39-,40-,42-,43+,47-,48?,49+/m0/s1
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
(1R,9R,16E,19S,20S,23R,24S,27R)-4,6,20,24,25-Pentahydroxy-27-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4,6-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (6Z,12Z)-octadeca-6,9,12-trienoic acidGenerator
Chemical FormulaC50H79N3O18P2
Average Molecular Weight1072.133
Monoisotopic Molecular Weight1071.483386712
IUPAC Name(1R,9R,16Z,19S,20S,23R,24S,25S,27R)-27-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,20,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (6Z,9Z,12Z)-octadeca-6,9,12-trienoate
Traditional Name(1R,9R,16Z,19S,20S,23R,24S,25S,27R)-27-(4-amino-2-oxopyrimidin-1-yl)-4,6,20,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (6Z,9Z,12Z)-octadeca-6,9,12-trienoate
CAS Registry NumberNot Available
SMILES
CCCCC\C=C/C\C=C/C\C=C/CCCCC(=O)O[C@@H]1COC(=O)CCC\C=C/C[C@H]2[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@H](O)[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OC1)O[C@H]2N1C=CC(N)=NC1=O
InChI Identifier
InChI=1S/C50H79N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-24-28-46(58)69-38-34-66-45(57)27-23-20-19-22-26-40-42(56)33-41(55)39(30-29-37(54)25-21-6-4-2)47(59)48(60)43(36-68-73(64,65)71-72(62,63)67-35-38)70-49(40)53-32-31-44(51)52-50(53)61/h9-10,12-13,15-16,19,22,29-32,37-40,42-43,47-49,54,56,59-60H,3-8,11,14,17-18,20-21,23-28,33-36H2,1-2H3,(H,62,63)(H,64,65)(H2,51,52,61)/b10-9-,13-12-,16-15-,22-19-,30-29+/t37-,38+,39-,40-,42-,43+,47-,48?,49+/m0/s1
InChI KeyDMEIAHFPIHHNAG-QJEJVIEYSA-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
logP3.77ALOGPS
logP6.18ChemAxon
logS-4.3ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)0.34ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area320.8 ŲChemAxon
Rotatable Bond Count22ChemAxon
Refractivity274.96 m³·mol⁻¹ChemAxon
Polarizability110.62 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]+312.21732859911
AllCCS[M+H-H2O]+312.73932859911
AllCCS[M+Na]+311.54232859911
AllCCS[M+NH4]+311.69832859911
AllCCS[M-H]-295.82932859911
AllCCS[M+Na-2H]-302.54632859911
AllCCS[M+HCOO]-309.82332859911
DeepCCS[M+H]+311.20130932474
DeepCCS[M-H]-309.43430932474
DeepCCS[M-2H]-343.46730932474
DeepCCS[M+Na]+317.33530932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/18:3(6Z,9Z,12Z)) 10V, Positive-QTOFsplash10-0w90-9400000001-c7a3d56ac30706270aad2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/18:3(6Z,9Z,12Z)) 20V, Positive-QTOFsplash10-06ri-9300000006-ca68a85961b89c08b5e62021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/18:3(6Z,9Z,12Z)) 40V, Positive-QTOFsplash10-00bc-4400001911-e8b74f2fa8ccc682462b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/18:3(6Z,9Z,12Z)) 10V, Negative-QTOFsplash10-00di-9000000000-f5988847de7847e7f38e2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/18:3(6Z,9Z,12Z)) 20V, Negative-QTOFsplash10-08ou-9330000721-e0594619a2ff788a20602021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/18:3(6Z,9Z,12Z)) 40V, Negative-QTOFsplash10-01ox-3300001900-ba5044fcc69d76bf0baa2021-10-21Wishart 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 ]