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Showing metabocard for CDP-DG(PGE2/20:3(5Z,8Z,11Z)) (HMDB0291932)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 03:34:21 UTC
Update Date2022-11-30 20:07:49 UTC
HMDB IDHMDB0291932
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(PGE2/20:3(5Z,8Z,11Z))
DescriptionCDP-DG(PGE2/20:3(5Z,8Z,11Z)) 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(PGE2/20:3(5Z,8Z,11Z)), in particular, consists of one chain of one Prostaglandin E2 at the C-1 position and one chain of 5Z,8Z,11Z-eicosatrienoyl 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 HMDB0291932 (CDP-DG(PGE2/20:3(5Z,8Z,11Z)))


  Mrv1652309172105342D          

 75 77  0  0  1  0            999 V2000
   -7.5900   -1.5435    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0291932 (CDP-DG(PGE2/20:3(5Z,8Z,11Z)))

HMDB0291932
     RDKit          3D
CDP-DG(PGE2/20:3(5Z,8Z,11Z))
158160  0  0  0  0  0  0  0  0999 V2000
   18.8715    0.2819   -0.3332 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5929    0.3001   -1.1508 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5939   -0.6553   -0.5757 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2664   -0.2821    0.8385 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6853    1.0987    0.8855 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4113    1.1917    0.0594 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3588    0.2572    0.5536 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1068    0.3965   -0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3679    0.0678   -1.7121 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7735   -0.8939   -2.3464 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7638   -1.7805   -1.7515 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5187   -1.6224   -2.5331 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3891   -1.2092   -2.0787 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1277   -0.8150   -0.6927 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0695   -1.6534   -0.0798 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0547    2.4000    1.4824 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8282    2.5595    0.6779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6439    3.6233   -0.0054 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8584    1.5861    0.6384 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7091    1.8021   -0.1553 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5322    1.9162    0.8053 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.4069   -0.1286   -0.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5216    0.6193   -1.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4291   -2.6348    0.5338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6881   -1.9998   -0.6212 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.1072   -3.0390   -1.5704 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0291932 (CDP-DG(PGE2/20:3(5Z,8Z,11Z)))


  Mrv1652309172105342D          

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    7.0202   11.0455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9148    3.0516    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.1475    2.8298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3122    3.6100    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.1218    3.8061    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  9 34  1  0  0  0  0
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 40 74  1  0  0  0  0
 74 75  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0291932

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCC\C=C/C\C=C/C\C=C/CCCC(=O)O[C@@H]1COC(=O)CCC\C=C/C[C@@H]2[C@@H](O[C@H](COP(O)(=O)OP(O)(=O)OC1)[C@@H](O)[C@@H](O)[C@@H](\C=C\[C@@H](O)CCCCC)[C@H](O)CC2=O)N1C=CC(N)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C52H83N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-19-20-26-30-48(60)71-40-36-68-47(59)29-25-22-21-24-28-42-44(58)35-43(57)41(32-31-39(56)27-23-6-4-2)49(61)50(62)45(38-70-75(66,67)73-74(64,65)69-37-40)72-51(42)55-34-33-46(53)54-52(55)63/h12-13,15-16,18-19,21,24,31-34,39-43,45,49-51,56-57,61-62H,3-11,14,17,20,22-23,25-30,35-38H2,1-2H3,(H,64,65)(H,66,67)(H2,53,54,63)/b13-12-,16-15-,19-18-,24-21-,32-31+/t39-,40+,41-,42-,43+,45+,49-,50?,51+/m0/s1

> <INCHI_KEY>
WLSFJBJZLOWQOM-MNXWZESCSA-N

> <FORMULA>
C52H83N3O18P2

> <MOLECULAR_WEIGHT>
1100.187

> <EXACT_MASS>
1099.514686841

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
158

> <JCHEM_AVERAGE_POLARIZABILITY>
117.45398679717735

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,9R,16Z,19R,22R,23S,24S,25S,27R)-27-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,22,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,20-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (5Z,8Z,11Z)-icosa-5,8,11-trienoate

> <ALOGPS_LOGP>
4.26

> <JCHEM_LOGP>
6.9667771944202315

> <ALOGPS_LOGS>
-4.49

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2718999239461373

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8697147678387385

> <JCHEM_PKA_STRONGEST_BASIC>
0.3038794608558414

> <JCHEM_POLAR_SURFACE_AREA>
320.8

> <JCHEM_REFRACTIVITY>
284.371

> <JCHEM_ROTATABLE_BOND_COUNT>
24

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.60e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,9R,16Z,19R,22R,23S,24S,25S,27R)-27-(4-amino-2-oxopyrimidin-1-yl)-4,6,22,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,20-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (5Z,8Z,11Z)-icosa-5,8,11-trienoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0291932 (CDP-DG(PGE2/20:3(5Z,8Z,11Z)))

HMDB0291932
     RDKit          3D
CDP-DG(PGE2/20:3(5Z,8Z,11Z))
158160  0  0  0  0  0  0  0  0999 V2000
   18.8715    0.2819   -0.3332 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5929    0.3001   -1.1508 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5939   -0.6553   -0.5757 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2664   -0.2821    0.8385 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6853    1.0987    0.8855 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4113    1.1917    0.0594 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3588    0.2572    0.5536 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1068    0.3965   -0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3679    0.0678   -1.7121 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7735   -0.8939   -2.3464 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7638   -1.7805   -1.7515 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5187   -1.6224   -2.5331 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3891   -1.2092   -2.0787 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1277   -0.8150   -0.6927 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0695   -1.6534   -0.0798 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9453   -1.1312    0.3537 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6206    0.2856    0.2801 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3825    0.9196    1.6615 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0547    2.4000    1.4824 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8282    2.5595    0.6779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6439    3.6233   -0.0054 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8584    1.5861    0.6384 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7091    1.8021   -0.1553 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5322    1.9162    0.8053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0547    3.2041    0.7702 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2354    3.5312    0.1638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7048    4.7020    0.1957 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0305    2.5166   -0.5679 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0816    3.1095   -1.4635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3285    2.2207   -1.4808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1410    1.0513   -2.3866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0815    0.1007   -2.3381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3538    0.2531   -1.5793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5730   -0.8166   -0.5591 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.0125   -1.1489   -0.3154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8494   -0.3720   -0.7655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4347   -2.3265    0.4143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9324   -2.2176    1.7839 C   0  0  1  0  0  0  0  0  0  0  0  0
   -9.1752   -3.5366    2.2662 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3286   -1.3476    2.7876 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.6808    0.0856    2.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6475    0.7618    2.9987 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9030    2.1641    2.5743 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.8578    2.6362    1.7847 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1699    2.1698    1.7381 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5057    3.5685    1.2628 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7654    3.5499    0.4365 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.1375    4.9276   -0.0572 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3984    4.9058   -0.8827 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9623   -1.4738    3.2665 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.3029   -0.2220    3.1176 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0441   -2.5112    2.7715 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.2007   -2.9702    3.8215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0750   -2.0465    1.6739 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6498   -2.5687    1.9798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9127   -2.7844    0.8527 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6121   -1.7740    0.6119 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.1882   -1.0308    1.8321 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0293   -0.7221   -0.6723 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3222   -2.7196    0.0015 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8021   -1.7621   -0.8233 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.2158   -2.0479   -0.3553 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7666   -2.1371   -2.4920 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4069   -0.1286   -0.6927 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5216    0.6193   -1.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4291   -2.6348    0.5338 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6881   -1.9998   -0.6212 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.1072   -3.0390   -1.5704 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8523   -2.8479   -2.6442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2326   -3.8399   -3.5234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8203   -5.1335   -3.2903 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1909   -6.1806   -4.1729 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0620   -5.3315   -2.1986 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7137   -4.3342   -1.3665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0025   -4.6705   -0.3879 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1380   -0.7240   -0.0013 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.7940    0.9206    0.5506 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.7068    0.6328   -1.0007 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.8638   -0.0481   -2.1931 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.2132    1.3220   -1.2793 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6656   -0.7253   -1.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.0618   -1.6703   -0.5704 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.1943   -0.3074    1.4621 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.5740   -1.0182    1.3120 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.4332    1.4085    1.9292 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.3954    1.8337    0.4864 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.6512    1.0284   -0.9937 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.0402    2.2298    0.1966 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7027   -0.8032    0.5401 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.0825    0.5353    1.5949 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2683   -0.1055    0.1666 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.8708    1.5024   -0.2518 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.1143    0.6914   -2.2371 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.0329   -1.0683   -3.3993 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.5953   -1.6889   -0.7010 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.1121   -2.8635   -1.9917 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5692   -1.8898   -3.6270 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5372   -1.1401   -2.7749 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9676    0.2743   -0.5836 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0478   -1.0036   -0.0682 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2305   -2.7465    0.0163 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2004   -1.8034    0.8007 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6082    0.3472   -0.2273 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2710    0.9517   -0.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5431    0.3897    2.1129 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2686    0.8134    2.3137 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8079    2.7693    2.5064 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8772    2.9481    1.0205 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7622    2.7631   -0.6856 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8276    1.7062    1.8534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3732    1.8980   -1.2017 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4872    1.8380    0.2089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4085    4.0720   -0.9981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7286    3.3199   -2.4760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4591    1.8852   -0.4307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1728    2.8527   -1.8306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2824    0.9831   -3.0481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8297   -0.7986   -2.9072 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2834    1.2952   -1.1235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2384    0.4183   -2.2675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2932   -0.2988    0.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2656   -2.7794   -0.2275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6865   -3.1736    0.3842 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0062   -1.8377    1.6860 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9232   -3.5063    3.2234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0106   -1.5124    3.7049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0975    0.5865    1.6764 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2435    0.2945    3.7593 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0269    2.8399    3.4643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9312    2.2663    0.8699 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0270    1.7842    2.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0253    1.4725    0.8911 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5301    4.2952    2.0760 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6806    3.8808    0.5756 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6115    3.1753    1.0630 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.6726    2.8572   -0.4080 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3077    5.3084   -0.6660 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.3432    5.5592    0.8421 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.3078    4.7570   -0.2591 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.5347    5.8622   -1.4232 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3895    4.1026   -1.6480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9510   -1.5583    4.4074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6861    0.4624    3.6878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5333   -3.4559    2.4442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6339   -2.2067    4.1273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9352   -0.9545    1.7127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1129   -1.8630    2.6420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8211   -3.4862    2.5853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8759   -1.1487   -1.5313 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1966   -2.9002   -2.6909 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3952   -0.0297   -1.1232 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3689    1.0331   -2.0911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7028   -1.6395   -1.0458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1921   -1.8624   -2.8604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8523   -3.6123   -4.3951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3431   -7.1295   -3.7758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3153   -6.0461   -5.1879 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
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 24 25  1  0
 25 26  1  0
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 26 28  1  0
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 31 32  2  0
 32 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  2  0
 35 37  1  0
 37 38  1  0
 38 39  1  0
 38 40  1  0
 40 41  1  0
 41 42  2  0
 42 43  1  0
 43 44  1  0
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 45 46  1  0
 46 47  1  0
 47 48  1  0
 48 49  1  0
 40 50  1  0
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 52 54  1  0
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 73 74  1  0
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 65 23  1  0
 74 68  1  0
 67 34  1  0
  1 76  1  0
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 67154  1  6
 69155  1  0
 70156  1  0
 72157  1  0
 72158  1  0
M  END
Download

PDB for HMDB0291932 (CDP-DG(PGE2/20:3(5Z,8Z,11Z)))

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     -14.168  -2.881   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0     -13.243  -1.576   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0     -13.854  -0.162   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0     -12.936   1.074   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0     -14.467   1.598   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0     -11.406   0.896   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0     -10.795  -0.517   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -11.713  -1.753   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0     -10.487   2.132   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0     -11.590   3.267   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0     -12.245   4.710   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -13.281   5.911   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0     -13.504   7.479   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0     -12.835   8.931   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0     -14.486   8.825   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0     -13.927  10.168   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0     -11.564   9.899   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0     -10.041  10.383   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0     -11.154  11.625   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -9.729  12.102   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -8.443  10.325   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -6.942   9.824   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.666   8.869   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.609   7.680   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -3.933   6.249   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -3.538   4.734   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -1.899   4.685   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -3.377   3.178   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.459   1.609   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.053   0.143   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.320  -0.787   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -6.886  -0.774   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -8.198   0.068   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -9.070   1.397   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -7.975   2.517   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -6.872   1.486   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -7.172   3.851   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -7.382   5.401   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -6.009   4.718   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -8.380   6.591   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -7.843   8.072   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -7.801   9.680   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -7.206  11.527   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      -8.255  12.929   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -6.156  12.863   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -5.647  14.435   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -4.121  14.991   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -3.129  16.202   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -1.609  15.953   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      -4.007   9.516   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      -2.288   9.682   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      -0.878   8.943   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0      -0.787  10.432   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       0.873  10.564   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       1.912  11.791   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       3.506  11.572   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       4.535  12.760   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       4.031  14.216   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       5.039  15.380   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       4.535  16.835   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       3.023  17.126   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       2.519  18.581   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       3.527  19.745   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0       5.039  19.454   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0       5.543  17.999   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0       7.055  17.708   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0       8.063  18.872   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0       9.576  18.581   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      10.584  19.745   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      12.096  19.454   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0      13.104  20.618   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0     -11.041   5.696   0.000  0.00  0.00           C+0
HETATM   73  O   UNK     0      -9.609   5.282   0.000  0.00  0.00           O+0
HETATM   74  C   UNK     0      -9.916   6.739   0.000  0.00  0.00           C+0
HETATM   75  O   UNK     0     -11.427   7.105   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   72                                                  
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   74                                                  
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   70                                                       
CONECT   70   69   71                                                       
CONECT   71   70                                                            
CONECT   72   11   73   74                                                  
CONECT   73   72                                                            
CONECT   74   72   40   75                                                  
CONECT   75   74                                                            
MASTER        0    0    0    0    0    0    0    0   75    0  154    0
END
Download

3D PDB for HMDB0291932 (CDP-DG(PGE2/20:3(5Z,8Z,11Z)))

COMPND    HMDB0291932
HETATM    1  C1  UNL     1      18.872   0.282  -0.333  1.00  0.00           C  
HETATM    2  C2  UNL     1      17.593   0.300  -1.151  1.00  0.00           C  
HETATM    3  C3  UNL     1      16.594  -0.655  -0.576  1.00  0.00           C  
HETATM    4  C4  UNL     1      16.266  -0.282   0.838  1.00  0.00           C  
HETATM    5  C5  UNL     1      15.685   1.099   0.885  1.00  0.00           C  
HETATM    6  C6  UNL     1      14.411   1.192   0.059  1.00  0.00           C  
HETATM    7  C7  UNL     1      13.359   0.257   0.554  1.00  0.00           C  
HETATM    8  C8  UNL     1      12.107   0.396  -0.311  1.00  0.00           C  
HETATM    9  C9  UNL     1      12.368   0.068  -1.712  1.00  0.00           C  
HETATM   10  C10 UNL     1      11.774  -0.894  -2.346  1.00  0.00           C  
HETATM   11  C11 UNL     1      10.764  -1.781  -1.752  1.00  0.00           C  
HETATM   12  C12 UNL     1       9.519  -1.622  -2.533  1.00  0.00           C  
HETATM   13  C13 UNL     1       8.389  -1.209  -2.079  1.00  0.00           C  
HETATM   14  C14 UNL     1       8.128  -0.815  -0.693  1.00  0.00           C  
HETATM   15  C15 UNL     1       7.070  -1.653  -0.080  1.00  0.00           C  
HETATM   16  C16 UNL     1       5.945  -1.131   0.354  1.00  0.00           C  
HETATM   17  C17 UNL     1       5.621   0.286   0.280  1.00  0.00           C  
HETATM   18  C18 UNL     1       5.383   0.920   1.662  1.00  0.00           C  
HETATM   19  C19 UNL     1       5.055   2.400   1.482  1.00  0.00           C  
HETATM   20  C20 UNL     1       3.828   2.559   0.678  1.00  0.00           C  
HETATM   21  O1  UNL     1       3.644   3.623  -0.005  1.00  0.00           O  
HETATM   22  O2  UNL     1       2.858   1.586   0.638  1.00  0.00           O  
HETATM   23  C21 UNL     1       1.709   1.802  -0.155  1.00  0.00           C  
HETATM   24  C22 UNL     1       0.532   1.916   0.805  1.00  0.00           C  
HETATM   25  O3  UNL     1      -0.055   3.204   0.770  1.00  0.00           O  
HETATM   26  C23 UNL     1      -1.235   3.531   0.164  1.00  0.00           C  
HETATM   27  O4  UNL     1      -1.705   4.702   0.196  1.00  0.00           O  
HETATM   28  C24 UNL     1      -2.030   2.517  -0.568  1.00  0.00           C  
HETATM   29  C25 UNL     1      -3.082   3.110  -1.464  1.00  0.00           C  
HETATM   30  C26 UNL     1      -4.328   2.221  -1.481  1.00  0.00           C  
HETATM   31  C27 UNL     1      -4.141   1.051  -2.387  1.00  0.00           C  
HETATM   32  C28 UNL     1      -5.081   0.101  -2.338  1.00  0.00           C  
HETATM   33  C29 UNL     1      -6.354   0.253  -1.579  1.00  0.00           C  
HETATM   34  C30 UNL     1      -6.573  -0.817  -0.559  1.00  0.00           C  
HETATM   35  C31 UNL     1      -8.012  -1.149  -0.315  1.00  0.00           C  
HETATM   36  O5  UNL     1      -8.849  -0.372  -0.765  1.00  0.00           O  
HETATM   37  C32 UNL     1      -8.435  -2.326   0.414  1.00  0.00           C  
HETATM   38  C33 UNL     1      -8.932  -2.218   1.784  1.00  0.00           C  
HETATM   39  O6  UNL     1      -9.175  -3.537   2.266  1.00  0.00           O  
HETATM   40  C34 UNL     1      -8.329  -1.348   2.788  1.00  0.00           C  
HETATM   41  C35 UNL     1      -8.681   0.086   2.437  1.00  0.00           C  
HETATM   42  C36 UNL     1      -9.648   0.762   2.999  1.00  0.00           C  
HETATM   43  C37 UNL     1      -9.903   2.164   2.574  1.00  0.00           C  
HETATM   44  O7  UNL     1      -8.858   2.636   1.785  1.00  0.00           O  
HETATM   45  C38 UNL     1     -11.170   2.170   1.738  1.00  0.00           C  
HETATM   46  C39 UNL     1     -11.506   3.568   1.263  1.00  0.00           C  
HETATM   47  C40 UNL     1     -12.765   3.550   0.437  1.00  0.00           C  
HETATM   48  C41 UNL     1     -13.137   4.928  -0.057  1.00  0.00           C  
HETATM   49  C42 UNL     1     -14.398   4.906  -0.883  1.00  0.00           C  
HETATM   50  C43 UNL     1      -6.962  -1.474   3.266  1.00  0.00           C  
HETATM   51  O8  UNL     1      -6.303  -0.222   3.118  1.00  0.00           O  
HETATM   52  C44 UNL     1      -6.044  -2.511   2.771  1.00  0.00           C  
HETATM   53  O9  UNL     1      -5.201  -2.970   3.821  1.00  0.00           O  
HETATM   54  C45 UNL     1      -5.075  -2.046   1.674  1.00  0.00           C  
HETATM   55  C46 UNL     1      -3.650  -2.569   1.980  1.00  0.00           C  
HETATM   56  O10 UNL     1      -2.913  -2.784   0.853  1.00  0.00           O  
HETATM   57  P1  UNL     1      -1.612  -1.774   0.612  1.00  0.00           P  
HETATM   58  O11 UNL     1      -1.188  -1.031   1.832  1.00  0.00           O  
HETATM   59  O12 UNL     1      -2.029  -0.722  -0.672  1.00  0.00           O  
HETATM   60  O13 UNL     1      -0.322  -2.720   0.001  1.00  0.00           O  
HETATM   61  P2  UNL     1       0.802  -1.762  -0.823  1.00  0.00           P  
HETATM   62  O14 UNL     1       2.216  -2.048  -0.355  1.00  0.00           O  
HETATM   63  O15 UNL     1       0.767  -2.137  -2.492  1.00  0.00           O  
HETATM   64  O16 UNL     1       0.407  -0.129  -0.693  1.00  0.00           O  
HETATM   65  C47 UNL     1       1.522   0.619  -1.058  1.00  0.00           C  
HETATM   66  O17 UNL     1      -5.429  -2.635   0.534  1.00  0.00           O  
HETATM   67  C48 UNL     1      -5.688  -2.000  -0.621  1.00  0.00           C  
HETATM   68  N1  UNL     1      -6.107  -3.039  -1.570  1.00  0.00           N  
HETATM   69  C49 UNL     1      -6.852  -2.848  -2.644  1.00  0.00           C  
HETATM   70  C50 UNL     1      -7.233  -3.840  -3.523  1.00  0.00           C  
HETATM   71  C51 UNL     1      -6.820  -5.133  -3.290  1.00  0.00           C  
HETATM   72  N2  UNL     1      -7.191  -6.181  -4.173  1.00  0.00           N  
HETATM   73  N3  UNL     1      -6.062  -5.332  -2.199  1.00  0.00           N  
HETATM   74  C52 UNL     1      -5.714  -4.334  -1.367  1.00  0.00           C  
HETATM   75  O18 UNL     1      -5.003  -4.671  -0.388  1.00  0.00           O  
HETATM   76  H1  UNL     1      19.138  -0.724  -0.001  1.00  0.00           H  
HETATM   77  H2  UNL     1      18.794   0.921   0.551  1.00  0.00           H  
HETATM   78  H3  UNL     1      19.707   0.633  -1.001  1.00  0.00           H  
HETATM   79  H4  UNL     1      17.864  -0.048  -2.193  1.00  0.00           H  
HETATM   80  H5  UNL     1      17.213   1.322  -1.279  1.00  0.00           H  
HETATM   81  H6  UNL     1      15.666  -0.725  -1.176  1.00  0.00           H  
HETATM   82  H7  UNL     1      17.062  -1.670  -0.570  1.00  0.00           H  
HETATM   83  H8  UNL     1      17.194  -0.307   1.462  1.00  0.00           H  
HETATM   84  H9  UNL     1      15.574  -1.018   1.312  1.00  0.00           H  
HETATM   85  H10 UNL     1      15.433   1.408   1.929  1.00  0.00           H  
HETATM   86  H11 UNL     1      16.395   1.834   0.486  1.00  0.00           H  
HETATM   87  H12 UNL     1      14.651   1.028  -0.994  1.00  0.00           H  
HETATM   88  H13 UNL     1      14.040   2.230   0.197  1.00  0.00           H  
HETATM   89  H14 UNL     1      13.703  -0.803   0.540  1.00  0.00           H  
HETATM   90  H15 UNL     1      13.082   0.535   1.595  1.00  0.00           H  
HETATM   91  H16 UNL     1      11.268  -0.106   0.167  1.00  0.00           H  
HETATM   92  H17 UNL     1      11.871   1.502  -0.252  1.00  0.00           H  
HETATM   93  H18 UNL     1      13.114   0.691  -2.237  1.00  0.00           H  
HETATM   94  H19 UNL     1      12.033  -1.068  -3.399  1.00  0.00           H  
HETATM   95  H20 UNL     1      10.595  -1.689  -0.701  1.00  0.00           H  
HETATM   96  H21 UNL     1      11.112  -2.863  -1.992  1.00  0.00           H  
HETATM   97  H22 UNL     1       9.569  -1.890  -3.627  1.00  0.00           H  
HETATM   98  H23 UNL     1       7.537  -1.140  -2.775  1.00  0.00           H  
HETATM   99  H24 UNL     1       7.968   0.274  -0.584  1.00  0.00           H  
HETATM  100  H25 UNL     1       9.048  -1.004  -0.068  1.00  0.00           H  
HETATM  101  H26 UNL     1       7.231  -2.746   0.016  1.00  0.00           H  
HETATM  102  H27 UNL     1       5.200  -1.803   0.801  1.00  0.00           H  
HETATM  103  H28 UNL     1       4.608   0.347  -0.227  1.00  0.00           H  
HETATM  104  H29 UNL     1       6.271   0.952  -0.259  1.00  0.00           H  
HETATM  105  H30 UNL     1       4.543   0.390   2.113  1.00  0.00           H  
HETATM  106  H31 UNL     1       6.269   0.813   2.314  1.00  0.00           H  
HETATM  107  H32 UNL     1       4.808   2.769   2.506  1.00  0.00           H  
HETATM  108  H33 UNL     1       5.877   2.948   1.021  1.00  0.00           H  
HETATM  109  H34 UNL     1       1.762   2.763  -0.686  1.00  0.00           H  
HETATM  110  H35 UNL     1      -0.260   1.193   0.530  1.00  0.00           H  
HETATM  111  H36 UNL     1       0.828   1.706   1.853  1.00  0.00           H  
HETATM  112  H37 UNL     1      -1.373   1.898  -1.202  1.00  0.00           H  
HETATM  113  H38 UNL     1      -2.487   1.838   0.209  1.00  0.00           H  
HETATM  114  H39 UNL     1      -3.408   4.072  -0.998  1.00  0.00           H  
HETATM  115  H40 UNL     1      -2.729   3.320  -2.476  1.00  0.00           H  
HETATM  116  H41 UNL     1      -4.459   1.885  -0.431  1.00  0.00           H  
HETATM  117  H42 UNL     1      -5.173   2.853  -1.831  1.00  0.00           H  
HETATM  118  H43 UNL     1      -3.282   0.983  -3.048  1.00  0.00           H  
HETATM  119  H44 UNL     1      -4.830  -0.799  -2.907  1.00  0.00           H  
HETATM  120  H45 UNL     1      -6.283   1.295  -1.123  1.00  0.00           H  
HETATM  121  H46 UNL     1      -7.238   0.418  -2.267  1.00  0.00           H  
HETATM  122  H47 UNL     1      -6.293  -0.299   0.412  1.00  0.00           H  
HETATM  123  H48 UNL     1      -9.266  -2.779  -0.227  1.00  0.00           H  
HETATM  124  H49 UNL     1      -7.687  -3.174   0.384  1.00  0.00           H  
HETATM  125  H50 UNL     1     -10.006  -1.838   1.686  1.00  0.00           H  
HETATM  126  H51 UNL     1      -8.923  -3.506   3.223  1.00  0.00           H  
HETATM  127  H52 UNL     1      -9.011  -1.512   3.705  1.00  0.00           H  
HETATM  128  H53 UNL     1      -8.097   0.586   1.676  1.00  0.00           H  
HETATM  129  H54 UNL     1     -10.243   0.295   3.759  1.00  0.00           H  
HETATM  130  H55 UNL     1     -10.027   2.840   3.464  1.00  0.00           H  
HETATM  131  H56 UNL     1      -8.931   2.266   0.870  1.00  0.00           H  
HETATM  132  H57 UNL     1     -12.027   1.784   2.325  1.00  0.00           H  
HETATM  133  H58 UNL     1     -11.025   1.473   0.891  1.00  0.00           H  
HETATM  134  H59 UNL     1     -11.530   4.295   2.076  1.00  0.00           H  
HETATM  135  H60 UNL     1     -10.681   3.881   0.576  1.00  0.00           H  
HETATM  136  H61 UNL     1     -13.611   3.175   1.063  1.00  0.00           H  
HETATM  137  H62 UNL     1     -12.673   2.857  -0.408  1.00  0.00           H  
HETATM  138  H63 UNL     1     -12.308   5.308  -0.666  1.00  0.00           H  
HETATM  139  H64 UNL     1     -13.343   5.559   0.842  1.00  0.00           H  
HETATM  140  H65 UNL     1     -15.308   4.757  -0.259  1.00  0.00           H  
HETATM  141  H66 UNL     1     -14.535   5.862  -1.423  1.00  0.00           H  
HETATM  142  H67 UNL     1     -14.389   4.103  -1.648  1.00  0.00           H  
HETATM  143  H68 UNL     1      -6.951  -1.558   4.407  1.00  0.00           H  
HETATM  144  H69 UNL     1      -6.686   0.462   3.688  1.00  0.00           H  
HETATM  145  H70 UNL     1      -6.533  -3.456   2.444  1.00  0.00           H  
HETATM  146  H71 UNL     1      -4.634  -2.207   4.127  1.00  0.00           H  
HETATM  147  H72 UNL     1      -4.935  -0.955   1.713  1.00  0.00           H  
HETATM  148  H73 UNL     1      -3.113  -1.863   2.642  1.00  0.00           H  
HETATM  149  H74 UNL     1      -3.821  -3.486   2.585  1.00  0.00           H  
HETATM  150  H75 UNL     1      -1.876  -1.149  -1.531  1.00  0.00           H  
HETATM  151  H76 UNL     1       0.197  -2.900  -2.691  1.00  0.00           H  
HETATM  152  H77 UNL     1       2.395  -0.030  -1.123  1.00  0.00           H  
HETATM  153  H78 UNL     1       1.369   1.033  -2.091  1.00  0.00           H  
HETATM  154  H79 UNL     1      -4.703  -1.640  -1.046  1.00  0.00           H  
HETATM  155  H80 UNL     1      -7.192  -1.862  -2.860  1.00  0.00           H  
HETATM  156  H81 UNL     1      -7.852  -3.612  -4.395  1.00  0.00           H  
HETATM  157  H82 UNL     1      -7.343  -7.130  -3.776  1.00  0.00           H  
HETATM  158  H83 UNL     1      -7.315  -6.046  -5.188  1.00  0.00           H  
CONECT    1    2   76   77   78
CONECT    2    3   79   80
CONECT    3    4   81   82
CONECT    4    5   83   84
CONECT    5    6   85   86
CONECT    6    7   87   88
CONECT    7    8   89   90
CONECT    8    9   91   92
CONECT    9   10   10   93
CONECT   10   11   94
CONECT   11   12   95   96
CONECT   12   13   13   97
CONECT   13   14   98
CONECT   14   15   99  100
CONECT   15   16   16  101
CONECT   16   17  102
CONECT   17   18  103  104
CONECT   18   19  105  106
CONECT   19   20  107  108
CONECT   20   21   21   22
CONECT   22   23
CONECT   23   24   65  109
CONECT   24   25  110  111
CONECT   25   26
CONECT   26   27   27   28
CONECT   28   29  112  113
CONECT   29   30  114  115
CONECT   30   31  116  117
CONECT   31   32   32  118
CONECT   32   33  119
CONECT   33   34  120  121
CONECT   34   35   67  122
CONECT   35   36   36   37
CONECT   37   38  123  124
CONECT   38   39   40  125
CONECT   39  126
CONECT   40   41   50  127
CONECT   41   42   42  128
CONECT   42   43  129
CONECT   43   44   45  130
CONECT   44  131
CONECT   45   46  132  133
CONECT   46   47  134  135
CONECT   47   48  136  137
CONECT   48   49  138  139
CONECT   49  140  141  142
CONECT   50   51   52  143
CONECT   51  144
CONECT   52   53   54  145
CONECT   53  146
CONECT   54   55   66  147
CONECT   55   56  148  149
CONECT   56   57
CONECT   57   58   58   59   60
CONECT   59  150
CONECT   60   61
CONECT   61   62   62   63   64
CONECT   63  151
CONECT   64   65
CONECT   65  152  153
CONECT   66   67
CONECT   67   68  154
CONECT   68   69   74
CONECT   69   70   70  155
CONECT   70   71  156
CONECT   71   72   73   73
CONECT   72  157  158
CONECT   73   74
CONECT   74   75   75
END
Download

SMILES for HMDB0291932 (CDP-DG(PGE2/20:3(5Z,8Z,11Z)))

CCCCCCCC\C=C/C\C=C/C\C=C/CCCC(=O)O[C@@H]1COC(=O)CCC\C=C/C[C@@H]2[C@@H](O[C@H](COP(O)(=O)OP(O)(=O)OC1)[C@@H](O)[C@@H](O)[C@@H](\C=C\[C@@H](O)CCCCC)[C@H](O)CC2=O)N1C=CC(N)=NC1=O
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INCHI for HMDB0291932 (CDP-DG(PGE2/20:3(5Z,8Z,11Z)))

InChI=1S/C52H83N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-19-20-26-30-48(60)71-40-36-68-47(59)29-25-22-21-24-28-42-44(58)35-43(57)41(32-31-39(56)27-23-6-4-2)49(61)50(62)45(38-70-75(66,67)73-74(64,65)69-37-40)72-51(42)55-34-33-46(53)54-52(55)63/h12-13,15-16,18-19,21,24,31-34,39-43,45,49-51,56-57,61-62H,3-11,14,17,20,22-23,25-30,35-38H2,1-2H3,(H,64,65)(H,66,67)(H2,53,54,63)/b13-12-,16-15-,19-18-,24-21-,32-31+/t39-,40+,41-,42-,43+,45+,49-,50?,51+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(1R,9R,16E,19R,22R,23S,24S,27R)-4,6,22,24,25-Pentahydroxy-27-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,20-tetraoxo-3,5,7,11,26-pentaoxa-4,6-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (5Z,8Z,11Z)-icosa-5,8,11-trienoic acidGenerator
Chemical FormulaC52H83N3O18P2
Average Molecular Weight1100.187
Monoisotopic Molecular Weight1099.514686841
IUPAC Name(1R,9R,16Z,19R,22R,23S,24S,25S,27R)-27-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,22,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,20-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (5Z,8Z,11Z)-icosa-5,8,11-trienoate
Traditional Name(1R,9R,16Z,19R,22R,23S,24S,25S,27R)-27-(4-amino-2-oxopyrimidin-1-yl)-4,6,22,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,20-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl (5Z,8Z,11Z)-icosa-5,8,11-trienoate
CAS Registry NumberNot Available
SMILES
CCCCCCCC\C=C/C\C=C/C\C=C/CCCC(=O)O[C@@H]1COC(=O)CCC\C=C/C[C@@H]2[C@@H](O[C@H](COP(O)(=O)OP(O)(=O)OC1)[C@@H](O)[C@@H](O)[C@@H](\C=C\[C@@H](O)CCCCC)[C@H](O)CC2=O)N1C=CC(N)=NC1=O
InChI Identifier
InChI=1S/C52H83N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-19-20-26-30-48(60)71-40-36-68-47(59)29-25-22-21-24-28-42-44(58)35-43(57)41(32-31-39(56)27-23-6-4-2)49(61)50(62)45(38-70-75(66,67)73-74(64,65)69-37-40)72-51(42)55-34-33-46(53)54-52(55)63/h12-13,15-16,18-19,21,24,31-34,39-43,45,49-51,56-57,61-62H,3-11,14,17,20,22-23,25-30,35-38H2,1-2H3,(H,64,65)(H,66,67)(H2,53,54,63)/b13-12-,16-15-,19-18-,24-21-,32-31+/t39-,40+,41-,42-,43+,45+,49-,50?,51+/m0/s1
InChI KeyWLSFJBJZLOWQOM-MNXWZESCSA-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
logP4.26ALOGPS
logP6.97ChemAxon
logS-4.5ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)0.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area320.8 ŲChemAxon
Rotatable Bond Count24ChemAxon
Refractivity284.37 m³·mol⁻¹ChemAxon
Polarizability117.45 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]+317.44532859911
AllCCS[M+H-H2O]+318.00332859911
AllCCS[M+Na]+316.72932859911
AllCCS[M+NH4]+316.89432859911
AllCCS[M-H]-297.66132859911
AllCCS[M+Na-2H]-304.18232859911
AllCCS[M+HCOO]-311.23132859911
DeepCCS[M+H]+305.47330932474
DeepCCS[M-H]-303.85230932474
DeepCCS[M-2H]-338.64130932474
DeepCCS[M+Na]+312.20630932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGE2/20:3(5Z,8Z,11Z)) 10V, Positive-QTOFsplash10-0il0-7900000000-e00675c6ae63539eeb222021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGE2/20:3(5Z,8Z,11Z)) 20V, Positive-QTOFsplash10-03di-9100000004-1770865c96c71d8867de2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGE2/20:3(5Z,8Z,11Z)) 40V, Positive-QTOFsplash10-01vy-4900000223-3c01459887292a96c5ae2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGE2/20:3(5Z,8Z,11Z)) 10V, Negative-QTOFsplash10-0002-9000000000-11cb595b98413632cd612021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGE2/20:3(5Z,8Z,11Z)) 20V, Negative-QTOFsplash10-03dm-9312001642-563f68c6f4f15a504d392021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGE2/20:3(5Z,8Z,11Z)) 40V, Negative-QTOFsplash10-0006-2300000900-a738fc6805b9963df9a42021-10-21Wishart 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 ]