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Showing metabocard for CDP-DG(16:0/6 keto-PGF1alpha) (HMDB0290792)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-16 18:58:09 UTC
Update Date2022-11-30 20:07:19 UTC
HMDB IDHMDB0290792
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(16:0/6 keto-PGF1alpha)
DescriptionCDP-DG(16:0/6 keto-PGF1alpha) 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(16:0/6 keto-PGF1alpha), in particular, consists of one chain of one hexadecanoyl at the C-1 position and one chain of 6-Keto-prostaglandin F1alpha 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 HMDB0290792 (CDP-DG(16:0/6 keto-PGF1alpha))


  Mrv1652309162120582D          

 72 74  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0290792 (CDP-DG(16:0/6 keto-PGF1alpha))

HMDB0290792
     RDKit          3D
CDP-DG(16:0/6 keto-PGF1alpha)
155157  0  0  0  0  0  0  0  0999 V2000
   14.3545    0.1928    2.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9525   -1.1421    3.4325 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5549   -1.3406    3.8151 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4205   -1.3545    2.9389 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9593   -0.3208    2.0394 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7044    0.0342    0.8209 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0009    1.1614    0.0519 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6477    0.7221   -0.3641 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9522    1.8295   -1.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7600    2.1461   -2.3967 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.7163    0.5782   -1.4530 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -8.2774    3.1818   -0.4887 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0108    2.6427    0.6562 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.4451    2.9657    1.9003 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4418    3.1319    0.5956 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0606    2.6601   -0.6948 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0869    1.1647   -0.8555 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7479    0.8183   -2.1784 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8030   -0.6727   -2.3958 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0905    2.1899    0.3302 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0524    1.7444   -0.5280 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0290792 (CDP-DG(16:0/6 keto-PGF1alpha))


  Mrv1652309162120582D          

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 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 23 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  2  0  0  0  0
 44 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  2  0  0  0  0
 50 52  1  0  0  0  0
 53 52  1  6  0  0  0
  9 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  1  0  0  0
 54 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  6  0  0  0
 57 59  1  0  0  0  0
 59 60  1  1  0  0  0
 60 61  2  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  6  0  0  0
 62 64  1  0  0  0  0
 64 65  1  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 67 68  1  0  0  0  0
 11 69  1  0  0  0  0
 69 70  1  6  0  0  0
 69 71  1  0  0  0  0
 59 71  1  0  0  0  0
 71 72  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0290792

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C48H83N3O19P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-18-23-43(56)65-31-36-32-66-71(61,62)70-72(63,64)67-33-41-46(59)45(58)37(26-25-34(52)21-17-6-4-2)39(54)30-40(55)38(29-35(53)22-19-20-24-44(57)68-36)47(69-41)51-28-27-42(49)50-48(51)60/h25-28,34,36-41,45-47,52,54-55,58-59H,3-24,29-33H2,1-2H3,(H,61,62)(H,63,64)(H2,49,50,60)/b26-25-/t34-,36+,37-,38-,39+,40-,41+,45?,46+,47+/m0/s1

> <INCHI_KEY>
HZGQWSFFNFVTFQ-QHRKWSLKSA-N

> <FORMULA>
C48H83N3O19P2

> <MOLECULAR_WEIGHT>
1068.142

> <EXACT_MASS>
1067.509601461

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
155

> <JCHEM_AVERAGE_POLARIZABILITY>
111.69776774384022

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1R,9R,18S,19S,21R,22S,23S,24S,26R)-26-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,19,21,23,24-hexahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,16-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacosan-9-yl]methyl hexadecanoate

> <ALOGPS_LOGP>
2.61

> <JCHEM_LOGP>
4.8327102199023075

> <ALOGPS_LOGS>
-3.66

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.271902101828823

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8697802094369766

> <JCHEM_PKA_STRONGEST_BASIC>
0.306545982232454

> <JCHEM_POLAR_SURFACE_AREA>
341.03000000000003

> <JCHEM_REFRACTIVITY>
263.02600000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
24

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.35e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,9R,18S,19S,21R,22S,23S,24S,26R)-26-(4-amino-2-oxopyrimidin-1-yl)-4,6,19,21,23,24-hexahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,16-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacosan-9-yl]methyl hexadecanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0290792 (CDP-DG(16:0/6 keto-PGF1alpha))

HMDB0290792
     RDKit          3D
CDP-DG(16:0/6 keto-PGF1alpha)
155157  0  0  0  0  0  0  0  0999 V2000
   14.3545    0.1928    2.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9525   -1.1421    3.4325 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5549   -1.3406    3.8151 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4205   -1.3545    2.9389 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9593   -0.3208    2.0394 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7044    0.0342    0.8209 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0009    1.1614    0.0519 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6477    0.7221   -0.3641 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9522    1.8295   -1.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7600    2.1461   -2.3967 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0518    1.0807   -3.3591 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9915    0.5018   -4.1774 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7828   -0.1053   -3.5487 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9448   -0.7644   -4.6483 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6863   -1.3840   -4.1968 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6943   -0.4533   -3.6446 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8885    0.7754   -3.4921 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4294   -0.9200   -3.2535 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4129   -0.1206   -2.7366 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7163    0.5782   -1.4530 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0209   -0.4550   -0.3408 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2173   -0.1445    0.7656 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1718   -1.3435    1.9183 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.2552   -1.0497    2.9483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5609   -2.8603    1.2669 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7105   -1.3525    2.7107 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0613    0.1459    2.8007 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.1005    0.6308    4.2432 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8484    1.2607    1.9407 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6093   -0.0705    2.1903 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5053    0.9480    2.5062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8117    0.5828    1.7599 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.4817   -0.3766    2.4012 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5870   -1.6411    1.9226 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.6571   -2.2672    2.7220 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7173   -1.5524    3.1482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7400   -2.0733    3.9089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6763   -3.4047    4.2543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6991   -4.0393    5.0494 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6155   -4.0880    3.8179 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6160   -3.5600    3.0701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6537   -4.3251    2.7188 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7520   -1.8169    0.4566 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8861   -3.0106    0.0264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1672   -2.7347   -1.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7128   -3.0349   -2.2960 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7987   -2.0981   -1.2332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8508   -0.7646   -1.9214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8969    0.2225   -1.2683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4297    1.2322   -2.2983 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6941    2.0185   -1.7372 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6764    3.2792   -1.9648 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6719    1.4178   -1.0255 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1178   -2.0106   -0.0697 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.8823   -2.8617    0.7269 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9151   -0.8021   -0.3515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2721    0.3699   -0.9775 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.9909    0.6654   -2.1713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4182    1.6429   -0.1337 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.0947    2.7348   -0.8622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2774    3.1818   -0.4887 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0108    2.6427    0.6562 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.4451    2.9657    1.9003 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4418    3.1319    0.5956 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0606    2.6601   -0.6948 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0869    1.1647   -0.8555 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7479    0.8183   -2.1784 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8030   -0.6727   -2.3958 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0905    2.1899    0.3302 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0524    1.7444   -0.5280 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6945    1.8410    1.7182 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9692    2.9267    2.2616 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.1488    0.6261    3.6265 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5162    0.9363    2.9973 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.7793    0.1394    1.9382 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.6165   -1.3829    4.3349 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.2950   -1.9103    2.6565 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4990   -2.3267    4.4629 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3146   -0.6053    4.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4580   -2.3523    2.2995 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4675   -1.6539    3.5792 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8759   -0.5900    1.7328 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7706    0.6363    2.6467 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.6565   -0.8462    0.0925 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7264    0.3415    0.9100 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8820    2.0368    0.7415 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.6350    1.5163   -0.7834 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9901    0.6498    0.5444 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6185   -0.2474   -0.8687 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0555    2.7391   -0.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9447    1.5613   -1.3548 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1689    2.9447   -2.9645 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7016    2.7296   -2.1189 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8910    1.4973   -4.0495 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6581    0.2502   -2.8224 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6750    1.2522   -4.9802 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4726   -0.3260   -4.8225 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1315    0.7293   -3.1561 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0116   -0.7827   -2.7279 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7591    0.0102   -5.4401 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6144   -1.5202   -5.1109 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2538   -1.9432   -5.0670 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9492   -2.1930   -3.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5150   -0.7691   -2.5836 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2077    0.6665   -3.5064 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6246    1.1939   -1.5850 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0679   -0.3920   -0.0154 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8262   -1.4761   -0.7151 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9592   -2.9813    0.4727 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7408    2.1881    2.2737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7061    0.9268    3.5884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1819    1.9207    2.1243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4598    0.4251    0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6454   -2.1731    2.2716 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8129   -0.4866    2.9002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5693   -1.4667    4.2296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5050   -4.4772    5.9605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6761   -4.0592    4.6894 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3039   -0.9870   -0.1393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5152   -3.8938   -0.1231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1247   -3.2501    0.7960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4467   -1.9714   -0.1957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0688   -2.7979   -1.7128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8846   -0.3813   -1.9383 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4923   -0.9134   -2.9689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0575   -0.3493   -0.8523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4002    0.8023   -0.4628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2769    1.9204   -2.5111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1756    0.7658   -3.2714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0103   -2.5639   -1.0551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2242   -3.6508    0.2593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8059   -1.1385   -0.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4180   -0.4359    0.5900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2422    0.2450   -1.3464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4572    1.3505   -2.6402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0028    1.4366    0.7822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5865    3.1847   -1.7424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6915    3.9895   -1.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0815    1.5142    0.6468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1701    2.7228    2.5555 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5318    4.2301    0.6846 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0359    2.6183    1.4090 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0553    3.1200   -0.8729 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4198    3.0386   -1.5451 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0424    0.7478   -0.9364 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5521    0.6243   -0.0136 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7689    1.2209   -2.1367 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1290    1.2490   -3.0006 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5202   -1.2383   -1.4828 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8421   -0.9506   -2.6395 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1707   -0.9837   -3.2477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0529    3.3106    0.2216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2637    2.0058   -1.4752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5596    1.6749    2.3898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8766    3.6531    1.6079 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  2  0
 23 25  1  0
 23 26  1  0
 26 27  1  0
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 27 29  1  0
 27 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
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 37 38  1  0
 38 39  1  0
 38 40  2  0
 40 41  1  0
 41 42  2  0
 34 43  1  0
 43 44  1  0
 44 45  1  0
 45 46  2  0
 45 47  1  0
 47 48  1  0
 48 49  1  0
 49 50  1  0
 50 51  1  0
 51 52  2  0
 51 53  1  0
 43 54  1  0
 54 55  1  0
 54 56  1  0
 56 57  1  0
 57 58  1  0
 57 59  1  0
 59 60  1  0
 60 61  2  0
 61 62  1  0
 62 63  1  0
 62 64  1  0
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 67 68  1  0
 59 69  1  0
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 69 71  1  0
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 53 20  1  0
 71 32  1  0
 41 35  1  0
  1 73  1  0
  1 74  1  0
  1 75  1  0
  2 76  1  0
  2 77  1  0
  3 78  1  0
  3 79  1  0
  4 80  1  0
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  5 82  1  0
  5 83  1  0
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  8 88  1  0
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 14100  1  0
 14101  1  0
 15102  1  0
 15103  1  0
 19104  1  0
 19105  1  0
 20106  1  6
 21107  1  0
 21108  1  0
 25109  1  0
 29110  1  0
 31111  1  0
 31112  1  0
 32113  1  6
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 67147  1  0
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 68149  1  0
 68150  1  0
 68151  1  0
 69152  1  1
 70153  1  0
 71154  1  1
 72155  1  0
M  END
Download

PDB for HMDB0290792 (CDP-DG(16:0/6 keto-PGF1alpha))

HEADER    PROTEIN                                 16-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-SEP-21         0                                  
HETATM    1  N   UNK     0      -5.036  -3.778   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -3.625  -3.009   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -3.698  -1.471   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -2.403  -0.638   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -3.434   0.608   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -1.034  -1.344   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -0.961  -2.882   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.256  -3.715   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.261  -0.511   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.422   0.939   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.103   2.466   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.782   3.940   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.226   4.726   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       3.803   5.232   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0       2.747   6.540   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.243   6.881   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.386   4.804   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       6.780   3.929   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       6.798   5.680   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       8.124   5.142   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       8.468   3.209   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       9.786   2.682   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.108   1.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      12.685   2.200   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      14.235   1.800   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      15.483   2.780   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      15.447   4.382   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      16.627   1.662   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      17.981   2.456   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      19.266   1.556   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      20.570   2.442   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      21.866   1.544   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      23.203   2.383   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      24.521   1.511   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      25.871   2.332   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      27.201   1.478   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      28.574   2.266   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      29.933   1.452   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      31.340   2.183   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      32.745   1.438   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      34.139   2.200   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      35.500   1.406   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      11.183   0.167   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      10.437  -1.265   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      11.641  -2.382   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0       9.557  -2.606   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       8.135  -3.361   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       6.599  -3.878   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       4.984  -3.966   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       3.377  -4.093   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       3.003  -5.669   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0       2.042  -3.186   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       1.304  -1.743   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       2.737  -1.095   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0       3.516   0.174   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0       4.264  -0.752   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       5.553   0.131   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0       6.887  -0.734   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0       4.790   1.493   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       6.333   1.584   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       7.211   2.718   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       8.042   4.304   0.000  0.00  0.00           C+0
HETATM   63  O   UNK     0       9.544   4.154   0.000  0.00  0.00           O+0
HETATM   64  C   UNK     0       8.008   6.279   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0       8.981   7.650   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0       8.486   9.233   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0       9.385  10.480   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0       8.754  11.884   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0       1.645   2.075   0.000  0.00  0.00           C+0
HETATM   70  O   UNK     0       0.686   0.947   0.000  0.00  0.00           O+0
HETATM   71  C   UNK     0       3.233   1.853   0.000  0.00  0.00           C+0
HETATM   72  O   UNK     0       2.379   3.188   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   53                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   69                                                  
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   43                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41                                                            
CONECT   43   23   44                                                       
CONECT   44   43   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50   53                                                       
CONECT   53   52    9   54                                                  
CONECT   54   53   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54   57                                                       
CONECT   57   56   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57   60   71                                                  
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63   64                                                  
CONECT   63   62                                                            
CONECT   64   62   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67                                                            
CONECT   69   11   70   71                                                  
CONECT   70   69                                                            
CONECT   71   69   59   72                                                  
CONECT   72   71                                                            
MASTER        0    0    0    0    0    0    0    0   72    0  148    0
END
Download

3D PDB for HMDB0290792 (CDP-DG(16:0/6 keto-PGF1alpha))

COMPND    HMDB0290792
HETATM    1  C1  UNL     1      14.355   0.193   2.954  1.00  0.00           C  
HETATM    2  C2  UNL     1      13.953  -1.142   3.432  1.00  0.00           C  
HETATM    3  C3  UNL     1      12.555  -1.341   3.815  1.00  0.00           C  
HETATM    4  C4  UNL     1      11.421  -1.355   2.939  1.00  0.00           C  
HETATM    5  C5  UNL     1      10.959  -0.321   2.039  1.00  0.00           C  
HETATM    6  C6  UNL     1      11.704   0.034   0.821  1.00  0.00           C  
HETATM    7  C7  UNL     1      11.001   1.161   0.052  1.00  0.00           C  
HETATM    8  C8  UNL     1       9.648   0.722  -0.364  1.00  0.00           C  
HETATM    9  C9  UNL     1       8.952   1.829  -1.188  1.00  0.00           C  
HETATM   10  C10 UNL     1       9.760   2.146  -2.397  1.00  0.00           C  
HETATM   11  C11 UNL     1      10.052   1.081  -3.359  1.00  0.00           C  
HETATM   12  C12 UNL     1       8.991   0.502  -4.177  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.783  -0.105  -3.549  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.945  -0.764  -4.648  1.00  0.00           C  
HETATM   15  C15 UNL     1       5.686  -1.384  -4.197  1.00  0.00           C  
HETATM   16  C16 UNL     1       4.694  -0.453  -3.645  1.00  0.00           C  
HETATM   17  O1  UNL     1       4.888   0.775  -3.492  1.00  0.00           O  
HETATM   18  O2  UNL     1       3.429  -0.920  -3.253  1.00  0.00           O  
HETATM   19  C17 UNL     1       2.413  -0.121  -2.737  1.00  0.00           C  
HETATM   20  C18 UNL     1       2.716   0.578  -1.453  1.00  0.00           C  
HETATM   21  C19 UNL     1       3.021  -0.455  -0.341  1.00  0.00           C  
HETATM   22  O3  UNL     1       2.217  -0.144   0.766  1.00  0.00           O  
HETATM   23  P1  UNL     1       2.172  -1.343   1.918  1.00  0.00           P  
HETATM   24  O4  UNL     1       3.255  -1.050   2.948  1.00  0.00           O  
HETATM   25  O5  UNL     1       2.561  -2.860   1.267  1.00  0.00           O  
HETATM   26  O6  UNL     1       0.711  -1.353   2.711  1.00  0.00           O  
HETATM   27  P2  UNL     1      -0.061   0.146   2.801  1.00  0.00           P  
HETATM   28  O7  UNL     1      -0.101   0.631   4.243  1.00  0.00           O  
HETATM   29  O8  UNL     1       0.848   1.261   1.941  1.00  0.00           O  
HETATM   30  O9  UNL     1      -1.609  -0.070   2.190  1.00  0.00           O  
HETATM   31  C20 UNL     1      -2.505   0.948   2.506  1.00  0.00           C  
HETATM   32  C21 UNL     1      -3.812   0.583   1.760  1.00  0.00           C  
HETATM   33  O10 UNL     1      -4.482  -0.377   2.401  1.00  0.00           O  
HETATM   34  C22 UNL     1      -4.587  -1.641   1.923  1.00  0.00           C  
HETATM   35  N1  UNL     1      -5.657  -2.267   2.722  1.00  0.00           N  
HETATM   36  C23 UNL     1      -6.717  -1.552   3.148  1.00  0.00           C  
HETATM   37  C24 UNL     1      -7.740  -2.073   3.909  1.00  0.00           C  
HETATM   38  C25 UNL     1      -7.676  -3.405   4.254  1.00  0.00           C  
HETATM   39  N2  UNL     1      -8.699  -4.039   5.049  1.00  0.00           N  
HETATM   40  N3  UNL     1      -6.615  -4.088   3.818  1.00  0.00           N  
HETATM   41  C26 UNL     1      -5.616  -3.560   3.070  1.00  0.00           C  
HETATM   42  O11 UNL     1      -4.654  -4.325   2.719  1.00  0.00           O  
HETATM   43  C27 UNL     1      -4.752  -1.817   0.457  1.00  0.00           C  
HETATM   44  C28 UNL     1      -3.886  -3.011   0.026  1.00  0.00           C  
HETATM   45  C29 UNL     1      -3.167  -2.735  -1.256  1.00  0.00           C  
HETATM   46  O12 UNL     1      -3.713  -3.035  -2.296  1.00  0.00           O  
HETATM   47  C30 UNL     1      -1.799  -2.098  -1.233  1.00  0.00           C  
HETATM   48  C31 UNL     1      -1.851  -0.765  -1.921  1.00  0.00           C  
HETATM   49  C32 UNL     1      -0.897   0.223  -1.268  1.00  0.00           C  
HETATM   50  C33 UNL     1      -0.430   1.232  -2.298  1.00  0.00           C  
HETATM   51  C34 UNL     1       0.694   2.018  -1.737  1.00  0.00           C  
HETATM   52  O13 UNL     1       0.676   3.279  -1.965  1.00  0.00           O  
HETATM   53  O14 UNL     1       1.672   1.418  -1.026  1.00  0.00           O  
HETATM   54  C35 UNL     1      -6.118  -2.011  -0.070  1.00  0.00           C  
HETATM   55  O15 UNL     1      -6.882  -2.862   0.727  1.00  0.00           O  
HETATM   56  C36 UNL     1      -6.915  -0.802  -0.351  1.00  0.00           C  
HETATM   57  C37 UNL     1      -6.272   0.370  -0.977  1.00  0.00           C  
HETATM   58  O16 UNL     1      -6.991   0.665  -2.171  1.00  0.00           O  
HETATM   59  C38 UNL     1      -6.418   1.643  -0.134  1.00  0.00           C  
HETATM   60  C39 UNL     1      -7.095   2.735  -0.862  1.00  0.00           C  
HETATM   61  C40 UNL     1      -8.277   3.182  -0.489  1.00  0.00           C  
HETATM   62  C41 UNL     1      -9.011   2.643   0.656  1.00  0.00           C  
HETATM   63  O17 UNL     1      -8.445   2.966   1.900  1.00  0.00           O  
HETATM   64  C42 UNL     1     -10.442   3.132   0.596  1.00  0.00           C  
HETATM   65  C43 UNL     1     -11.061   2.660  -0.695  1.00  0.00           C  
HETATM   66  C44 UNL     1     -11.087   1.165  -0.856  1.00  0.00           C  
HETATM   67  C45 UNL     1     -11.748   0.818  -2.178  1.00  0.00           C  
HETATM   68  C46 UNL     1     -11.803  -0.673  -2.396  1.00  0.00           C  
HETATM   69  C47 UNL     1      -5.090   2.190   0.330  1.00  0.00           C  
HETATM   70  O18 UNL     1      -4.052   1.744  -0.528  1.00  0.00           O  
HETATM   71  C48 UNL     1      -4.694   1.841   1.718  1.00  0.00           C  
HETATM   72  O19 UNL     1      -3.969   2.927   2.262  1.00  0.00           O  
HETATM   73  H1  UNL     1      15.149   0.626   3.626  1.00  0.00           H  
HETATM   74  H2  UNL     1      13.516   0.936   2.997  1.00  0.00           H  
HETATM   75  H3  UNL     1      14.779   0.139   1.938  1.00  0.00           H  
HETATM   76  H4  UNL     1      14.616  -1.383   4.335  1.00  0.00           H  
HETATM   77  H5  UNL     1      14.295  -1.910   2.656  1.00  0.00           H  
HETATM   78  H6  UNL     1      12.499  -2.327   4.463  1.00  0.00           H  
HETATM   79  H7  UNL     1      12.315  -0.605   4.707  1.00  0.00           H  
HETATM   80  H8  UNL     1      11.458  -2.352   2.300  1.00  0.00           H  
HETATM   81  H9  UNL     1      10.468  -1.654   3.579  1.00  0.00           H  
HETATM   82  H10 UNL     1       9.876  -0.590   1.733  1.00  0.00           H  
HETATM   83  H11 UNL     1      10.771   0.636   2.647  1.00  0.00           H  
HETATM   84  H12 UNL     1      11.657  -0.846   0.093  1.00  0.00           H  
HETATM   85  H13 UNL     1      12.726   0.342   0.910  1.00  0.00           H  
HETATM   86  H14 UNL     1      10.882   2.037   0.742  1.00  0.00           H  
HETATM   87  H15 UNL     1      11.635   1.516  -0.783  1.00  0.00           H  
HETATM   88  H16 UNL     1       8.990   0.650   0.544  1.00  0.00           H  
HETATM   89  H17 UNL     1       9.619  -0.247  -0.869  1.00  0.00           H  
HETATM   90  H18 UNL     1       9.055   2.739  -0.501  1.00  0.00           H  
HETATM   91  H19 UNL     1       7.945   1.561  -1.355  1.00  0.00           H  
HETATM   92  H20 UNL     1       9.169   2.945  -2.964  1.00  0.00           H  
HETATM   93  H21 UNL     1      10.702   2.730  -2.119  1.00  0.00           H  
HETATM   94  H22 UNL     1      10.891   1.497  -4.049  1.00  0.00           H  
HETATM   95  H23 UNL     1      10.658   0.250  -2.822  1.00  0.00           H  
HETATM   96  H24 UNL     1       8.675   1.252  -4.980  1.00  0.00           H  
HETATM   97  H25 UNL     1       9.473  -0.326  -4.822  1.00  0.00           H  
HETATM   98  H26 UNL     1       7.131   0.729  -3.156  1.00  0.00           H  
HETATM   99  H27 UNL     1       8.012  -0.783  -2.728  1.00  0.00           H  
HETATM  100  H28 UNL     1       6.759   0.010  -5.440  1.00  0.00           H  
HETATM  101  H29 UNL     1       7.614  -1.520  -5.111  1.00  0.00           H  
HETATM  102  H30 UNL     1       5.254  -1.943  -5.067  1.00  0.00           H  
HETATM  103  H31 UNL     1       5.949  -2.193  -3.469  1.00  0.00           H  
HETATM  104  H32 UNL     1       1.515  -0.769  -2.584  1.00  0.00           H  
HETATM  105  H33 UNL     1       2.208   0.667  -3.506  1.00  0.00           H  
HETATM  106  H34 UNL     1       3.625   1.194  -1.585  1.00  0.00           H  
HETATM  107  H35 UNL     1       4.068  -0.392  -0.015  1.00  0.00           H  
HETATM  108  H36 UNL     1       2.826  -1.476  -0.715  1.00  0.00           H  
HETATM  109  H37 UNL     1       1.959  -2.981   0.473  1.00  0.00           H  
HETATM  110  H38 UNL     1       0.741   2.188   2.274  1.00  0.00           H  
HETATM  111  H39 UNL     1      -2.706   0.927   3.588  1.00  0.00           H  
HETATM  112  H40 UNL     1      -2.182   1.921   2.124  1.00  0.00           H  
HETATM  113  H41 UNL     1      -3.460   0.425   0.734  1.00  0.00           H  
HETATM  114  H42 UNL     1      -3.645  -2.173   2.272  1.00  0.00           H  
HETATM  115  H43 UNL     1      -6.813  -0.487   2.900  1.00  0.00           H  
HETATM  116  H44 UNL     1      -8.569  -1.467   4.230  1.00  0.00           H  
HETATM  117  H45 UNL     1      -8.505  -4.477   5.961  1.00  0.00           H  
HETATM  118  H46 UNL     1      -9.676  -4.059   4.689  1.00  0.00           H  
HETATM  119  H47 UNL     1      -4.304  -0.987  -0.139  1.00  0.00           H  
HETATM  120  H48 UNL     1      -4.515  -3.894  -0.123  1.00  0.00           H  
HETATM  121  H49 UNL     1      -3.125  -3.250   0.796  1.00  0.00           H  
HETATM  122  H50 UNL     1      -1.447  -1.971  -0.196  1.00  0.00           H  
HETATM  123  H51 UNL     1      -1.069  -2.798  -1.713  1.00  0.00           H  
HETATM  124  H52 UNL     1      -2.885  -0.381  -1.938  1.00  0.00           H  
HETATM  125  H53 UNL     1      -1.492  -0.913  -2.969  1.00  0.00           H  
HETATM  126  H54 UNL     1      -0.058  -0.349  -0.852  1.00  0.00           H  
HETATM  127  H55 UNL     1      -1.400   0.802  -0.463  1.00  0.00           H  
HETATM  128  H56 UNL     1      -1.277   1.920  -2.511  1.00  0.00           H  
HETATM  129  H57 UNL     1      -0.176   0.766  -3.271  1.00  0.00           H  
HETATM  130  H58 UNL     1      -6.010  -2.564  -1.055  1.00  0.00           H  
HETATM  131  H59 UNL     1      -7.224  -3.651   0.259  1.00  0.00           H  
HETATM  132  H60 UNL     1      -7.806  -1.139  -0.965  1.00  0.00           H  
HETATM  133  H61 UNL     1      -7.418  -0.436   0.590  1.00  0.00           H  
HETATM  134  H62 UNL     1      -5.242   0.245  -1.346  1.00  0.00           H  
HETATM  135  H63 UNL     1      -6.457   1.350  -2.640  1.00  0.00           H  
HETATM  136  H64 UNL     1      -7.003   1.437   0.782  1.00  0.00           H  
HETATM  137  H65 UNL     1      -6.586   3.185  -1.742  1.00  0.00           H  
HETATM  138  H66 UNL     1      -8.692   3.989  -1.086  1.00  0.00           H  
HETATM  139  H67 UNL     1      -9.082   1.514   0.647  1.00  0.00           H  
HETATM  140  H68 UNL     1      -9.170   2.723   2.555  1.00  0.00           H  
HETATM  141  H69 UNL     1     -10.532   4.230   0.685  1.00  0.00           H  
HETATM  142  H70 UNL     1     -11.036   2.618   1.409  1.00  0.00           H  
HETATM  143  H71 UNL     1     -12.055   3.120  -0.873  1.00  0.00           H  
HETATM  144  H72 UNL     1     -10.420   3.039  -1.545  1.00  0.00           H  
HETATM  145  H73 UNL     1     -10.042   0.748  -0.936  1.00  0.00           H  
HETATM  146  H74 UNL     1     -11.552   0.624  -0.014  1.00  0.00           H  
HETATM  147  H75 UNL     1     -12.769   1.221  -2.137  1.00  0.00           H  
HETATM  148  H76 UNL     1     -11.129   1.249  -3.001  1.00  0.00           H  
HETATM  149  H77 UNL     1     -11.520  -1.238  -1.483  1.00  0.00           H  
HETATM  150  H78 UNL     1     -12.842  -0.951  -2.640  1.00  0.00           H  
HETATM  151  H79 UNL     1     -11.171  -0.984  -3.248  1.00  0.00           H  
HETATM  152  H80 UNL     1      -5.053   3.311   0.222  1.00  0.00           H  
HETATM  153  H81 UNL     1      -4.264   2.006  -1.475  1.00  0.00           H  
HETATM  154  H82 UNL     1      -5.560   1.675   2.390  1.00  0.00           H  
HETATM  155  H83 UNL     1      -3.877   3.653   1.608  1.00  0.00           H  
CONECT    1    2   73   74   75
CONECT    2    3   76   77
CONECT    3    4   78   79
CONECT    4    5   80   81
CONECT    5    6   82   83
CONECT    6    7   84   85
CONECT    7    8   86   87
CONECT    8    9   88   89
CONECT    9   10   90   91
CONECT   10   11   92   93
CONECT   11   12   94   95
CONECT   12   13   96   97
CONECT   13   14   98   99
CONECT   14   15  100  101
CONECT   15   16  102  103
CONECT   16   17   17   18
CONECT   18   19
CONECT   19   20  104  105
CONECT   20   21   53  106
CONECT   21   22  107  108
CONECT   22   23
CONECT   23   24   24   25   26
CONECT   25  109
CONECT   26   27
CONECT   27   28   28   29   30
CONECT   29  110
CONECT   30   31
CONECT   31   32  111  112
CONECT   32   33   71  113
CONECT   33   34
CONECT   34   35   43  114
CONECT   35   36   41
CONECT   36   37   37  115
CONECT   37   38  116
CONECT   38   39   40   40
CONECT   39  117  118
CONECT   40   41
CONECT   41   42   42
CONECT   43   44   54  119
CONECT   44   45  120  121
CONECT   45   46   46   47
CONECT   47   48  122  123
CONECT   48   49  124  125
CONECT   49   50  126  127
CONECT   50   51  128  129
CONECT   51   52   52   53
CONECT   54   55   56  130
CONECT   55  131
CONECT   56   57  132  133
CONECT   57   58   59  134
CONECT   58  135
CONECT   59   60   69  136
CONECT   60   61   61  137
CONECT   61   62  138
CONECT   62   63   64  139
CONECT   63  140
CONECT   64   65  141  142
CONECT   65   66  143  144
CONECT   66   67  145  146
CONECT   67   68  147  148
CONECT   68  149  150  151
CONECT   69   70   71  152
CONECT   70  153
CONECT   71   72  154
CONECT   72  155
END
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SMILES for HMDB0290792 (CDP-DG(16:0/6 keto-PGF1alpha))

CCCCCCCCCCCCCCCC(=O)OC[C@@H]1COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@@H](CC(=O)CCCCC(=O)O1)[C@@H](O)C[C@@H](O)[C@H](\C=C/[C@@H](O)CCCCC)[C@H](O)[C@@H]2O)N1C=CC(N)=NC1=O
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INCHI for HMDB0290792 (CDP-DG(16:0/6 keto-PGF1alpha))

InChI=1S/C48H83N3O19P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-18-23-43(56)65-31-36-32-66-71(61,62)70-72(63,64)67-33-41-46(59)45(58)37(26-25-34(52)21-17-6-4-2)39(54)30-40(55)38(29-35(53)22-19-20-24-44(57)68-36)47(69-41)51-28-27-42(49)50-48(51)60/h25-28,34,36-41,45-47,52,54-55,58-59H,3-24,29-33H2,1-2H3,(H,61,62)(H,63,64)(H2,49,50,60)/b26-25-/t34-,36+,37-,38-,39+,40-,41+,45?,46+,47+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[(1R,9R,18S,19S,21R,22S,24S,26R)-4,6,19,21,23,24-Hexahydroxy-26-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-22-[(1Z,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,16-tetraoxo-3,5,7,10,25-pentaoxa-4,6-diphosphabicyclo[16.6.2]hexacosan-9-yl]methyl hexadecanoic acidHMDB
Chemical FormulaC48H83N3O19P2
Average Molecular Weight1068.142
Monoisotopic Molecular Weight1067.509601461
IUPAC Name[(1R,9R,18S,19S,21R,22S,23S,24S,26R)-26-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,19,21,23,24-hexahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,16-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacosan-9-yl]methyl hexadecanoate
Traditional Name[(1R,9R,18S,19S,21R,22S,23S,24S,26R)-26-(4-amino-2-oxopyrimidin-1-yl)-4,6,19,21,23,24-hexahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,16-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacosan-9-yl]methyl hexadecanoate
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCC(=O)OC[C@@H]1COP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@@H](CC(=O)CCCCC(=O)O1)[C@@H](O)C[C@@H](O)[C@H](\C=C/[C@@H](O)CCCCC)[C@H](O)[C@@H]2O)N1C=CC(N)=NC1=O
InChI Identifier
InChI=1S/C48H83N3O19P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-18-23-43(56)65-31-36-32-66-71(61,62)70-72(63,64)67-33-41-46(59)45(58)37(26-25-34(52)21-17-6-4-2)39(54)30-40(55)38(29-35(53)22-19-20-24-44(57)68-36)47(69-41)51-28-27-42(49)50-48(51)60/h25-28,34,36-41,45-47,52,54-55,58-59H,3-24,29-33H2,1-2H3,(H,61,62)(H,63,64)(H2,49,50,60)/b26-25-/t34-,36+,37-,38-,39+,40-,41+,45?,46+,47+/m0/s1
InChI KeyHZGQWSFFNFVTFQ-QHRKWSLKSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Glycerophospholipid
  • Organic pyrophosphate
  • Hydroxypyrimidine
  • Fatty acid ester
  • Fatty acyl
  • Pyrimidine
  • Organic phosphoric acid derivative
  • Hydropyrimidine
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Cyclic ketone
  • Secondary alcohol
  • Lactone
  • Ketone
  • Carboxylic acid ester
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Polyol
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
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
logP2.61ALOGPS
logP4.83ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)0.31ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area341.03 ŲChemAxon
Rotatable Bond Count24ChemAxon
Refractivity263.03 m³·mol⁻¹ChemAxon
Polarizability111.7 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]+310.93932859911
AllCCS[M+H-H2O]+311.4532859911
AllCCS[M+Na]+310.28132859911
AllCCS[M+NH4]+310.43332859911
AllCCS[M-H]-314.71332859911
AllCCS[M+Na-2H]-320.61232859911
AllCCS[M+HCOO]-327.04932859911
DeepCCS[M+H]+311.39530932474
DeepCCS[M-H]-309.67230932474
DeepCCS[M-2H]-344.09630932474
DeepCCS[M+Na]+317.90330932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/6 keto-PGF1alpha) 10V, Positive-QTOFsplash10-0wn9-9300000000-9a65d117978921c1a85e2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/6 keto-PGF1alpha) 20V, Positive-QTOFsplash10-0f89-9000000006-2339432a7638dec958272021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/6 keto-PGF1alpha) 40V, Positive-QTOFsplash10-022a-9500000640-a83a975f6814ce50dd552021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/6 keto-PGF1alpha) 10V, Negative-QTOFsplash10-014i-9000000000-7658c5befd558bca9cfd2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/6 keto-PGF1alpha) 20V, Negative-QTOFsplash10-07vi-9130000031-491506f2943b86ba3f3e2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/6 keto-PGF1alpha) 40V, Negative-QTOFsplash10-08fr-9540000221-4cb32fa69ef2eb4b167f2021-10-21Wishart 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 ]