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Showing metabocard for CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)) (HMDB0294094)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 19:21:52 UTC
Update Date2022-11-30 20:08:52 UTC
HMDB IDHMDB0294094
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20))
DescriptionCDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)) 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(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)), in particular, consists of one chain of one 18-methylnonadecanoyl at the C-1 position and one chain of 20-Hydroxyeicosatetraenoyl 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 HMDB0294094 (CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)))

CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20))
  Mrv1652309172121222D          

 74 75  0  0  1  0            999 V2000
   -3.8020    0.3607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0969    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.6679    0.7716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9699   -0.3554    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7950   -0.3554    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.0908   -1.0682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.9068    0.3718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1918    0.7835    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
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 73 74  1  0  0  0  0
M  END
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3D MOL for HMDB0294094 (CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)))

HMDB0294094
     RDKit          3D
CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20))
162163  0  0  0  0  0  0  0  0999 V2000
   -4.4145    5.0299   -0.1553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8847    4.2041   -1.3028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8413    4.3865   -2.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8982    2.7384   -0.9061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3695    1.8861   -2.0310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3980    0.4260   -1.6135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8612   -0.4656   -2.7093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9057   -1.9112   -2.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3989   -2.8405   -3.3092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5026   -4.3156   -2.8768 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0312   -5.1961   -4.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5899   -5.0246   -4.3005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3461   -5.5676   -3.2235 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7928   -5.2466   -3.6494 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1004   -3.7987   -3.4959 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2048   -3.4086   -1.9807 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4009   -4.1041   -1.4414 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8051   -3.9193   -0.0627 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0403   -4.3851    1.0778 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7196   -3.8158    1.3400 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6965   -4.4230    0.9372 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5850   -2.6095    2.0461 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3893   -2.0299    2.3762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4384   -1.6951    1.1505 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3456   -0.6958    0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2217   -0.2197   -0.7744 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.0323    2.2360   -0.3470 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.7661    3.5337   -3.9740 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2005    3.7656   -5.3535 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3452    3.7690   -6.3895 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7419    3.9874   -7.6970 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0835    4.2133   -7.9533 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5355    4.4449   -9.2948 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9332    4.2070   -6.8993 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.5043    3.9903   -5.6415 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.5803    4.8699   -3.3298 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.0730    4.7618   -2.0138 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0700    5.0067   -3.3374 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -4.2838    0.0450    2.5585 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7166    0.1099    3.9325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2987   -0.1230    4.1038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8150   -1.1120    4.8291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5602   -2.1138    5.5674 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2895   -2.3143    6.9760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1541   -2.1806    7.9357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5445   -1.7874    7.8227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0532   -0.8568    8.8337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4504    0.3737    8.7382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4374    1.1626    7.4771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8487    2.4853    7.8764 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7225    2.9482    7.4860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7457    2.3204    6.5914 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0294094 (CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)))

CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20))
  Mrv1652309172121222D          

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  -10.8724   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6974   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4115   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -13.9506   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.6647   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -15.3789   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.0930   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -17.5212    0.4434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 73 74  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0294094

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C52H89N3O16P2/c1-43(2)34-30-26-22-18-14-10-7-8-11-15-19-23-27-31-35-47(57)66-40-44(69-48(58)36-32-28-24-20-16-12-6-4-3-5-9-13-17-21-25-29-33-39-56)41-67-72(62,63)71-73(64,65)68-42-45-49(59)50(60)51(70-45)55-38-37-46(53)54-52(55)61/h3,5-6,12-13,17,20,24,37-38,43-45,49-51,56,59-60H,4,7-11,14-16,18-19,21-23,25-36,39-42H2,1-2H3,(H,62,63)(H,64,65)(H2,53,54,61)/b5-3-,12-6-,17-13-,24-20-/t44-,45-,49-,50-,51-/m1/s1

> <INCHI_KEY>
HRNZMPZRUSUBIW-BAMXKHNKSA-N

> <FORMULA>
C52H89N3O16P2

> <MOLECULAR_WEIGHT>
1074.237

> <EXACT_MASS>
1073.571807794

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
162

> <JCHEM_AVERAGE_POLARIZABILITY>
118.042763612022

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-2-{[(5Z,8Z,11Z,14Z)-20-hydroxyicosa-5,8,11,14-tetraenoyl]oxy}-3-[(18-methylnonadecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
6.99

> <JCHEM_LOGP>
10.071384286666667

> <ALOGPS_LOGS>
-5.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2716279189544712

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8632255796955306

> <JCHEM_PKA_STRONGEST_BASIC>
-0.027317444798551582

> <JCHEM_POLAR_SURFACE_AREA>
283.50000000000006

> <JCHEM_REFRACTIVITY>
283.3612

> <JCHEM_ROTATABLE_BOND_COUNT>
46

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.37e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-2-{[(5Z,8Z,11Z,14Z)-20-hydroxyicosa-5,8,11,14-tetraenoyl]oxy}-3-[(18-methylnonadecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0294094 (CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)))

HMDB0294094
     RDKit          3D
CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20))
162163  0  0  0  0  0  0  0  0999 V2000
   -4.4145    5.0299   -0.1553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8847    4.2041   -1.3028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8413    4.3865   -2.4772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8982    2.7384   -0.9061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3695    1.8861   -2.0310 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3980    0.4260   -1.6135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8612   -0.4656   -2.7093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9057   -1.9112   -2.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3989   -2.8405   -3.3092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5026   -4.3156   -2.8768 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0312   -5.1961   -4.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5899   -5.0246   -4.3005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3461   -5.5676   -3.2235 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7928   -5.2466   -3.6494 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1004   -3.7987   -3.4959 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2048   -3.4086   -1.9807 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4009   -4.1041   -1.4414 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8051   -3.9193   -0.0627 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0403   -4.3851    1.0778 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7196   -3.8158    1.3400 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6965   -4.4230    0.9372 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5850   -2.6095    2.0461 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3893   -2.0299    2.3762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4384   -1.6951    1.1505 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3456   -0.6958    0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2217   -0.2197   -0.7744 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8487    0.9338   -1.4421 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.2213    0.3615   -1.6822 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0323    2.2360   -0.3470 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2733    1.5855   -2.8684 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3964    1.6039   -4.1038 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.3622    0.2189   -4.7565 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9317    2.7170   -5.3062 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9497    1.9803   -3.6213 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2339    3.3394   -3.6734 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6613    3.5542   -3.2153 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5684    2.8826   -4.0133 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7661    3.5337   -3.9740 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2005    3.7656   -5.3535 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3452    3.7690   -6.3895 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7419    3.9874   -7.6970 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0835    4.2133   -7.9533 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5355    4.4449   -9.2948 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.9332    4.2070   -6.8993 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.5043    3.9903   -5.6415 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3199    3.9884   -4.6627 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5803    4.8699   -3.3298 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.0730    4.7618   -2.0138 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0700    5.0067   -3.3374 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6140    5.7834   -2.2823 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6863   -1.1242    1.5575 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8784   -1.7414    1.4479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8827   -2.9307    0.9687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1909   -1.2155    1.8079 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2838    0.0450    2.5585 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7166    0.1099    3.9325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2987   -0.1230    4.1038 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8150   -1.1120    4.8291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5602   -2.1138    5.5674 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2895   -2.3143    6.9760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1541   -2.1806    7.9357 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5445   -1.7874    7.8227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0532   -0.8568    8.8337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4504    0.3737    8.7382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4374    1.1626    7.4771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8487    2.4853    7.8764 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7225    2.9482    7.4860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7457    2.3204    6.5914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4354    2.2994    7.4224 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2890    1.7123    6.6863 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9660    1.7693    7.5611 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7867    1.0030    8.8392 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9261    1.0453    9.6395 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0975    5.8104   -0.5452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5775    5.5411    0.3601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9731    4.3618    0.5201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8812    4.5301   -1.6497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3641    4.1098   -3.4186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7551    3.7757   -2.3236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1179    5.4547   -2.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2859    2.6380    0.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9273    2.4675   -0.6613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0497    2.0640   -2.9033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3450    2.1801   -2.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8664    0.3085   -0.6717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4670    0.1108   -1.4396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8369   -0.1550   -2.9710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4697   -0.3457   -3.6416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9119   -2.1724   -1.9115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1918   -2.0211   -1.3835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3499   -2.6229   -3.5790 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0142   -2.7303   -4.2341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5698   -4.5138   -2.6683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8946   -4.5030   -1.9745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6709   -5.0860   -4.9086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1789   -6.2702   -3.6982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3861   -5.6079   -5.2616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3621   -3.9815   -4.5518 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2635   -6.6704   -3.2087 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1215   -5.1768   -2.2290 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8177   -5.4544   -4.7549 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4725   -5.9509   -3.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0901   -3.6062   -3.9255 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3211   -3.1699   -3.9107 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2566   -3.6559   -1.5169 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3891   -2.3280   -2.0044 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.2771   -3.7996   -2.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0015   -2.7734    0.1325 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8738   -4.3405    0.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6297   -4.1766    2.0528 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9483   -5.5350    1.0930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1579   -2.7119    3.0637 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3389   -1.1912    0.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6330    0.1208    1.0859 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7948    2.0635    0.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0552    3.1362   -5.0871 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0593    3.7891   -4.6510 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5621    3.8423   -2.9308 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7963    3.2507   -2.1667 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5818    2.9248   -3.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2813    3.5889   -6.1792 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0202    3.9820   -8.4950 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2135    5.2765   -9.8549 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2007    3.8022   -9.7726 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0861    5.7023   -3.8690 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3465    4.6947   -1.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7574    5.3772   -4.3192 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3161    6.4096   -1.9333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7370   -1.0432    0.8151 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8232   -2.0381    2.2596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9074    0.8803    1.9034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3891    0.2898    2.6450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9241    1.2017    4.2576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3879   -0.4389    4.6548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5556    0.5470    3.6345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6891   -1.1971    4.9039 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2622   -3.1210    5.0674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6547   -2.0644    5.3352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2582   -2.6052    7.2454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7913   -2.3926    8.9679 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2089   -2.7106    7.8612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8059   -1.3417    6.8280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1196   -1.2751    9.9089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8374    0.9106    9.6517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8707    0.6692    6.7007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4794    1.2940    7.0854 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4979    3.0978    8.5936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4041    3.9660    7.8561 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5930    2.7917    5.6201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9549    1.2393    6.4346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6897    1.7904    8.3520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2155    3.3867    7.6011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4979    0.6228    6.5663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0760    2.1607    5.7208 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7836    1.3198    6.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2382    2.8140    7.7914 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4178   -0.0248    8.6790 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0127    1.5096    9.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5981    0.3747    9.4330 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
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 72160  1  0
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 73162  1  0
M  END
Download

PDB for HMDB0294094 (CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)))

HEADER    PROTEIN                                 17-SEP-21   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20))         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-21         0                                  
HETATM    1  O   UNK     0      -7.097   0.673   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.781   1.440   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.447   0.670   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.113   1.440   0.000  0.00  0.00           C+0
HETATM    5  H   UNK     0      -3.677  -0.663   0.000  0.00  0.00           H+0
HETATM    6  O   UNK     0      -5.217  -0.663   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       9.112  -2.009   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.770  -1.994   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.894   1.462   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.559   0.694   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       2.225   1.462   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       0.890   0.694   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      -0.456   1.444   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -1.790   0.671   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.290   2.790   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.251   2.763   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.997   2.801   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.456   2.801   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      11.394  -0.846   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      14.067   3.776   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      11.394   0.692   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0      12.729   1.463   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      12.729   3.005   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.394   3.776   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.059   3.005   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      10.059   1.463   0.000  0.00  0.00           N+0
HETATM   27  O   UNK     0       7.473   1.619   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.720   0.712   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.244  -0.754   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.702  -0.754   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.225   0.712   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -8.423   1.436   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -8.423   2.876   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -9.756   0.665   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -11.089   1.436   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -12.422   0.665   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -13.755   1.436   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -15.088   0.665   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -16.421   1.436   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -17.754   0.665   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -19.087   1.436   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -20.420   0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -21.753   1.436   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -23.086   0.665   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -24.419   1.436   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -25.752   0.665   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -27.085   1.436   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -28.418   0.665   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -29.751   1.436   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -31.084   0.665   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -32.417   1.436   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -32.417  -0.103   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -6.551  -1.383   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      -6.551  -2.823   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0      -7.884  -0.612   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -9.217  -1.383   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -10.550  -0.612   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -11.883  -1.383   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -13.423  -1.383   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -14.756  -0.612   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -16.089  -1.383   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -17.629  -1.383   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -18.962  -0.612   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -20.295  -1.383   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -21.835  -1.383   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -23.168  -0.612   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -24.501  -1.383   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0     -26.041  -1.383   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0     -27.374  -0.612   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0     -28.707  -1.383   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0     -30.040  -0.612   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0     -31.373  -1.383   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0     -32.706  -0.612   0.000  0.00  0.00           C+0
HETATM   74  O   UNK     0     -32.706   0.828   0.000  0.00  0.00           O+0
CONECT    1   32    2                                                       
CONECT    2    1    3                                                       
CONECT    3    2    5    6    4                                             
CONECT    4    3   14                                                       
CONECT    5    3                                                            
CONECT    6    3   53                                                       
CONECT    7   29                                                            
CONECT    8   30                                                            
CONECT    9   10   31                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   17   18                                             
CONECT   12   11   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13    4                                                       
CONECT   15   13                                                            
CONECT   16   13                                                            
CONECT   17   11                                                            
CONECT   18   11                                                            
CONECT   19   21                                                            
CONECT   20   23                                                            
CONECT   21   22   19   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   20                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   21   28                                                  
CONECT   27   28   31                                                       
CONECT   28   27   29   26                                                  
CONECT   29   28   30    7                                                  
CONECT   30   29   31    8                                                  
CONECT   31   27   30    9                                                  
CONECT   32    1   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50                                                            
CONECT   53    6   54   55                                                  
CONECT   54   53                                                            
CONECT   55   53   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   72                                                       
CONECT   72   71   73                                                       
CONECT   73   72   74                                                       
CONECT   74   73                                                            
MASTER        0    0    0    0    0    0    0    0   74    0  150    0
END
Download

3D PDB for HMDB0294094 (CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)))

COMPND    HMDB0294094
HETATM    1  C1  UNL     1      -4.414   5.030  -0.155  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.885   4.204  -1.303  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.841   4.387  -2.477  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.898   2.738  -0.906  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.369   1.886  -2.031  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.398   0.426  -1.613  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.861  -0.466  -2.709  1.00  0.00           C  
HETATM    8  C8  UNL     1      -2.906  -1.911  -2.246  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.399  -2.841  -3.309  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.503  -4.316  -2.877  1.00  0.00           C  
HETATM   11  C11 UNL     1      -2.031  -5.196  -4.003  1.00  0.00           C  
HETATM   12  C12 UNL     1      -0.590  -5.025  -4.300  1.00  0.00           C  
HETATM   13  C13 UNL     1       0.346  -5.568  -3.224  1.00  0.00           C  
HETATM   14  C14 UNL     1       1.793  -5.247  -3.649  1.00  0.00           C  
HETATM   15  C15 UNL     1       2.100  -3.799  -3.496  1.00  0.00           C  
HETATM   16  C16 UNL     1       2.205  -3.409  -1.981  1.00  0.00           C  
HETATM   17  C17 UNL     1       3.401  -4.104  -1.441  1.00  0.00           C  
HETATM   18  C18 UNL     1       3.805  -3.919  -0.063  1.00  0.00           C  
HETATM   19  C19 UNL     1       3.040  -4.385   1.078  1.00  0.00           C  
HETATM   20  C20 UNL     1       1.720  -3.816   1.340  1.00  0.00           C  
HETATM   21  O1  UNL     1       0.696  -4.423   0.937  1.00  0.00           O  
HETATM   22  O2  UNL     1       1.585  -2.610   2.046  1.00  0.00           O  
HETATM   23  C21 UNL     1       0.389  -2.030   2.376  1.00  0.00           C  
HETATM   24  C22 UNL     1      -0.438  -1.695   1.151  1.00  0.00           C  
HETATM   25  C23 UNL     1       0.346  -0.696   0.373  1.00  0.00           C  
HETATM   26  O3  UNL     1      -0.222  -0.220  -0.774  1.00  0.00           O  
HETATM   27  P1  UNL     1       0.849   0.934  -1.442  1.00  0.00           P  
HETATM   28  O4  UNL     1       2.221   0.362  -1.682  1.00  0.00           O  
HETATM   29  O5  UNL     1       1.032   2.236  -0.347  1.00  0.00           O  
HETATM   30  O6  UNL     1       0.273   1.585  -2.868  1.00  0.00           O  
HETATM   31  P2  UNL     1       1.396   1.604  -4.104  1.00  0.00           P  
HETATM   32  O7  UNL     1       1.362   0.219  -4.757  1.00  0.00           O  
HETATM   33  O8  UNL     1       0.932   2.717  -5.306  1.00  0.00           O  
HETATM   34  O9  UNL     1       2.950   1.980  -3.621  1.00  0.00           O  
HETATM   35  C24 UNL     1       3.234   3.339  -3.673  1.00  0.00           C  
HETATM   36  C25 UNL     1       4.661   3.554  -3.215  1.00  0.00           C  
HETATM   37  O10 UNL     1       5.568   2.883  -4.013  1.00  0.00           O  
HETATM   38  C26 UNL     1       6.766   3.534  -3.974  1.00  0.00           C  
HETATM   39  N1  UNL     1       7.200   3.766  -5.353  1.00  0.00           N  
HETATM   40  C27 UNL     1       6.345   3.769  -6.389  1.00  0.00           C  
HETATM   41  C28 UNL     1       6.742   3.987  -7.697  1.00  0.00           C  
HETATM   42  C29 UNL     1       8.083   4.213  -7.953  1.00  0.00           C  
HETATM   43  N2  UNL     1       8.535   4.445  -9.295  1.00  0.00           N  
HETATM   44  N3  UNL     1       8.933   4.207  -6.899  1.00  0.00           N  
HETATM   45  C30 UNL     1       8.504   3.990  -5.642  1.00  0.00           C  
HETATM   46  O11 UNL     1       9.320   3.988  -4.663  1.00  0.00           O  
HETATM   47  C31 UNL     1       6.580   4.870  -3.330  1.00  0.00           C  
HETATM   48  O12 UNL     1       7.073   4.762  -2.014  1.00  0.00           O  
HETATM   49  C32 UNL     1       5.070   5.007  -3.337  1.00  0.00           C  
HETATM   50  O13 UNL     1       4.614   5.783  -2.282  1.00  0.00           O  
HETATM   51  O14 UNL     1      -1.686  -1.124   1.558  1.00  0.00           O  
HETATM   52  C33 UNL     1      -2.878  -1.741   1.448  1.00  0.00           C  
HETATM   53  O15 UNL     1      -2.883  -2.931   0.969  1.00  0.00           O  
HETATM   54  C34 UNL     1      -4.191  -1.215   1.808  1.00  0.00           C  
HETATM   55  C35 UNL     1      -4.284   0.045   2.558  1.00  0.00           C  
HETATM   56  C36 UNL     1      -3.717   0.110   3.932  1.00  0.00           C  
HETATM   57  C37 UNL     1      -2.299  -0.123   4.104  1.00  0.00           C  
HETATM   58  C38 UNL     1      -1.815  -1.112   4.829  1.00  0.00           C  
HETATM   59  C39 UNL     1      -2.560  -2.114   5.567  1.00  0.00           C  
HETATM   60  C40 UNL     1      -2.290  -2.314   6.976  1.00  0.00           C  
HETATM   61  C41 UNL     1      -3.154  -2.181   7.936  1.00  0.00           C  
HETATM   62  C42 UNL     1      -4.545  -1.787   7.823  1.00  0.00           C  
HETATM   63  C43 UNL     1      -5.053  -0.857   8.834  1.00  0.00           C  
HETATM   64  C44 UNL     1      -5.450   0.374   8.738  1.00  0.00           C  
HETATM   65  C45 UNL     1      -5.437   1.163   7.477  1.00  0.00           C  
HETATM   66  C46 UNL     1      -4.849   2.485   7.876  1.00  0.00           C  
HETATM   67  C47 UNL     1      -3.723   2.948   7.486  1.00  0.00           C  
HETATM   68  C48 UNL     1      -2.746   2.320   6.591  1.00  0.00           C  
HETATM   69  C49 UNL     1      -1.435   2.299   7.422  1.00  0.00           C  
HETATM   70  C50 UNL     1      -0.289   1.712   6.686  1.00  0.00           C  
HETATM   71  C51 UNL     1       0.966   1.769   7.561  1.00  0.00           C  
HETATM   72  C52 UNL     1       0.787   1.003   8.839  1.00  0.00           C  
HETATM   73  O16 UNL     1       1.926   1.045   9.639  1.00  0.00           O  
HETATM   74  H1  UNL     1      -5.097   5.810  -0.545  1.00  0.00           H  
HETATM   75  H2  UNL     1      -3.578   5.541   0.360  1.00  0.00           H  
HETATM   76  H3  UNL     1      -4.973   4.362   0.520  1.00  0.00           H  
HETATM   77  H4  UNL     1      -2.881   4.530  -1.650  1.00  0.00           H  
HETATM   78  H5  UNL     1      -4.364   4.110  -3.419  1.00  0.00           H  
HETATM   79  H6  UNL     1      -5.755   3.776  -2.324  1.00  0.00           H  
HETATM   80  H7  UNL     1      -5.118   5.455  -2.546  1.00  0.00           H  
HETATM   81  H8  UNL     1      -3.286   2.638   0.023  1.00  0.00           H  
HETATM   82  H9  UNL     1      -4.927   2.467  -0.661  1.00  0.00           H  
HETATM   83  H10 UNL     1      -4.050   2.064  -2.903  1.00  0.00           H  
HETATM   84  H11 UNL     1      -2.345   2.180  -2.308  1.00  0.00           H  
HETATM   85  H12 UNL     1      -2.866   0.308  -0.672  1.00  0.00           H  
HETATM   86  H13 UNL     1      -4.467   0.111  -1.440  1.00  0.00           H  
HETATM   87  H14 UNL     1      -1.837  -0.155  -2.971  1.00  0.00           H  
HETATM   88  H15 UNL     1      -3.470  -0.346  -3.642  1.00  0.00           H  
HETATM   89  H16 UNL     1      -3.912  -2.172  -1.912  1.00  0.00           H  
HETATM   90  H17 UNL     1      -2.192  -2.021  -1.384  1.00  0.00           H  
HETATM   91  H18 UNL     1      -1.350  -2.623  -3.579  1.00  0.00           H  
HETATM   92  H19 UNL     1      -3.014  -2.730  -4.234  1.00  0.00           H  
HETATM   93  H20 UNL     1      -3.570  -4.514  -2.668  1.00  0.00           H  
HETATM   94  H21 UNL     1      -1.895  -4.503  -1.974  1.00  0.00           H  
HETATM   95  H22 UNL     1      -2.671  -5.086  -4.909  1.00  0.00           H  
HETATM   96  H23 UNL     1      -2.179  -6.270  -3.698  1.00  0.00           H  
HETATM   97  H24 UNL     1      -0.386  -5.608  -5.262  1.00  0.00           H  
HETATM   98  H25 UNL     1      -0.362  -3.981  -4.552  1.00  0.00           H  
HETATM   99  H26 UNL     1       0.263  -6.670  -3.209  1.00  0.00           H  
HETATM  100  H27 UNL     1       0.121  -5.177  -2.229  1.00  0.00           H  
HETATM  101  H28 UNL     1       1.818  -5.454  -4.755  1.00  0.00           H  
HETATM  102  H29 UNL     1       2.473  -5.951  -3.179  1.00  0.00           H  
HETATM  103  H30 UNL     1       3.090  -3.606  -3.925  1.00  0.00           H  
HETATM  104  H31 UNL     1       1.321  -3.170  -3.911  1.00  0.00           H  
HETATM  105  H32 UNL     1       1.257  -3.656  -1.517  1.00  0.00           H  
HETATM  106  H33 UNL     1       2.389  -2.328  -2.004  1.00  0.00           H  
HETATM  107  H34 UNL     1       3.329  -5.236  -1.647  1.00  0.00           H  
HETATM  108  H35 UNL     1       4.277  -3.800  -2.127  1.00  0.00           H  
HETATM  109  H36 UNL     1       4.002  -2.773   0.133  1.00  0.00           H  
HETATM  110  H37 UNL     1       4.874  -4.341   0.081  1.00  0.00           H  
HETATM  111  H38 UNL     1       3.630  -4.177   2.053  1.00  0.00           H  
HETATM  112  H39 UNL     1       2.948  -5.535   1.093  1.00  0.00           H  
HETATM  113  H40 UNL     1      -0.158  -2.712   3.064  1.00  0.00           H  
HETATM  114  H41 UNL     1       0.599  -1.078   2.927  1.00  0.00           H  
HETATM  115  H42 UNL     1      -0.582  -2.629   0.603  1.00  0.00           H  
HETATM  116  H43 UNL     1       1.339  -1.191   0.134  1.00  0.00           H  
HETATM  117  H44 UNL     1       0.633   0.121   1.086  1.00  0.00           H  
HETATM  118  H45 UNL     1       1.795   2.063   0.261  1.00  0.00           H  
HETATM  119  H46 UNL     1       0.055   3.136  -5.087  1.00  0.00           H  
HETATM  120  H47 UNL     1       3.059   3.789  -4.651  1.00  0.00           H  
HETATM  121  H48 UNL     1       2.562   3.842  -2.931  1.00  0.00           H  
HETATM  122  H49 UNL     1       4.796   3.251  -2.167  1.00  0.00           H  
HETATM  123  H50 UNL     1       7.582   2.925  -3.516  1.00  0.00           H  
HETATM  124  H51 UNL     1       5.281   3.589  -6.179  1.00  0.00           H  
HETATM  125  H52 UNL     1       6.020   3.982  -8.495  1.00  0.00           H  
HETATM  126  H53 UNL     1       8.213   5.276  -9.855  1.00  0.00           H  
HETATM  127  H54 UNL     1       9.201   3.802  -9.773  1.00  0.00           H  
HETATM  128  H55 UNL     1       7.086   5.702  -3.869  1.00  0.00           H  
HETATM  129  H56 UNL     1       6.347   4.695  -1.359  1.00  0.00           H  
HETATM  130  H57 UNL     1       4.757   5.377  -4.319  1.00  0.00           H  
HETATM  131  H58 UNL     1       5.316   6.410  -1.933  1.00  0.00           H  
HETATM  132  H59 UNL     1      -4.737  -1.043   0.815  1.00  0.00           H  
HETATM  133  H60 UNL     1      -4.823  -2.038   2.260  1.00  0.00           H  
HETATM  134  H61 UNL     1      -3.907   0.880   1.903  1.00  0.00           H  
HETATM  135  H62 UNL     1      -5.389   0.290   2.645  1.00  0.00           H  
HETATM  136  H63 UNL     1      -3.924   1.202   4.258  1.00  0.00           H  
HETATM  137  H64 UNL     1      -4.388  -0.439   4.655  1.00  0.00           H  
HETATM  138  H65 UNL     1      -1.556   0.547   3.634  1.00  0.00           H  
HETATM  139  H66 UNL     1      -0.689  -1.197   4.904  1.00  0.00           H  
HETATM  140  H67 UNL     1      -2.262  -3.121   5.067  1.00  0.00           H  
HETATM  141  H68 UNL     1      -3.655  -2.064   5.335  1.00  0.00           H  
HETATM  142  H69 UNL     1      -1.258  -2.605   7.245  1.00  0.00           H  
HETATM  143  H70 UNL     1      -2.791  -2.393   8.968  1.00  0.00           H  
HETATM  144  H71 UNL     1      -5.209  -2.711   7.861  1.00  0.00           H  
HETATM  145  H72 UNL     1      -4.806  -1.342   6.828  1.00  0.00           H  
HETATM  146  H73 UNL     1      -5.120  -1.275   9.909  1.00  0.00           H  
HETATM  147  H74 UNL     1      -5.837   0.911   9.652  1.00  0.00           H  
HETATM  148  H75 UNL     1      -4.871   0.669   6.701  1.00  0.00           H  
HETATM  149  H76 UNL     1      -6.479   1.294   7.085  1.00  0.00           H  
HETATM  150  H77 UNL     1      -5.498   3.098   8.594  1.00  0.00           H  
HETATM  151  H78 UNL     1      -3.404   3.966   7.856  1.00  0.00           H  
HETATM  152  H79 UNL     1      -2.593   2.792   5.620  1.00  0.00           H  
HETATM  153  H80 UNL     1      -2.955   1.239   6.435  1.00  0.00           H  
HETATM  154  H81 UNL     1      -1.690   1.790   8.352  1.00  0.00           H  
HETATM  155  H82 UNL     1      -1.215   3.387   7.601  1.00  0.00           H  
HETATM  156  H83 UNL     1      -0.498   0.623   6.566  1.00  0.00           H  
HETATM  157  H84 UNL     1      -0.076   2.161   5.721  1.00  0.00           H  
HETATM  158  H85 UNL     1       1.784   1.320   6.983  1.00  0.00           H  
HETATM  159  H86 UNL     1       1.238   2.814   7.791  1.00  0.00           H  
HETATM  160  H87 UNL     1       0.418  -0.025   8.679  1.00  0.00           H  
HETATM  161  H88 UNL     1      -0.013   1.510   9.454  1.00  0.00           H  
HETATM  162  H89 UNL     1       2.598   0.375   9.433  1.00  0.00           H  
CONECT    1    2   74   75   76
CONECT    2    3    4   77
CONECT    3   78   79   80
CONECT    4    5   81   82
CONECT    5    6   83   84
CONECT    6    7   85   86
CONECT    7    8   87   88
CONECT    8    9   89   90
CONECT    9   10   91   92
CONECT   10   11   93   94
CONECT   11   12   95   96
CONECT   12   13   97   98
CONECT   13   14   99  100
CONECT   14   15  101  102
CONECT   15   16  103  104
CONECT   16   17  105  106
CONECT   17   18  107  108
CONECT   18   19  109  110
CONECT   19   20  111  112
CONECT   20   21   21   22
CONECT   22   23
CONECT   23   24  113  114
CONECT   24   25   51  115
CONECT   25   26  116  117
CONECT   26   27
CONECT   27   28   28   29   30
CONECT   29  118
CONECT   30   31
CONECT   31   32   32   33   34
CONECT   33  119
CONECT   34   35
CONECT   35   36  120  121
CONECT   36   37   49  122
CONECT   37   38
CONECT   38   39   47  123
CONECT   39   40   45
CONECT   40   41   41  124
CONECT   41   42  125
CONECT   42   43   44   44
CONECT   43  126  127
CONECT   44   45
CONECT   45   46   46
CONECT   47   48   49  128
CONECT   48  129
CONECT   49   50  130
CONECT   50  131
CONECT   51   52
CONECT   52   53   53   54
CONECT   54   55  132  133
CONECT   55   56  134  135
CONECT   56   57  136  137
CONECT   57   58   58  138
CONECT   58   59  139
CONECT   59   60  140  141
CONECT   60   61   61  142
CONECT   61   62  143
CONECT   62   63  144  145
CONECT   63   64   64  146
CONECT   64   65  147
CONECT   65   66  148  149
CONECT   66   67   67  150
CONECT   67   68  151
CONECT   68   69  152  153
CONECT   69   70  154  155
CONECT   70   71  156  157
CONECT   71   72  158  159
CONECT   72   73  160  161
CONECT   73  162
END
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SMILES for HMDB0294094 (CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)))

[H][C@@](COC(=O)CCCCCCCCCCCCCCCCC(C)C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCCO
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INCHI for HMDB0294094 (CDP-DG(i-20:0/20:4(5Z,8Z,11Z,14Z)-OH(20)))

InChI=1S/C52H89N3O16P2/c1-43(2)34-30-26-22-18-14-10-7-8-11-15-19-23-27-31-35-47(57)66-40-44(69-48(58)36-32-28-24-20-16-12-6-4-3-5-9-13-17-21-25-29-33-39-56)41-67-72(62,63)71-73(64,65)68-42-45-49(59)50(60)51(70-45)55-38-37-46(53)54-52(55)61/h3,5-6,12-13,17,20,24,37-38,43-45,49-51,56,59-60H,4,7-11,14-16,18-19,21-23,25-36,39-42H2,1-2H3,(H,62,63)(H,64,65)(H2,53,54,61)/b5-3-,12-6-,17-13-,24-20-/t44-,45-,49-,50-,51-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-2-{[(5Z,8Z,11Z,14Z)-20-hydroxyicosa-5,8,11,14-tetraenoyl]oxy}-3-[(18-methylnonadecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinateGenerator
Chemical FormulaC52H89N3O16P2
Average Molecular Weight1074.237
Monoisotopic Molecular Weight1073.571807794
IUPAC Name{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-2-{[(5Z,8Z,11Z,14Z)-20-hydroxyicosa-5,8,11,14-tetraenoyl]oxy}-3-[(18-methylnonadecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-2-{[(5Z,8Z,11Z,14Z)-20-hydroxyicosa-5,8,11,14-tetraenoyl]oxy}-3-[(18-methylnonadecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCCCCCC(C)C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCCO
InChI Identifier
InChI=1S/C52H89N3O16P2/c1-43(2)34-30-26-22-18-14-10-7-8-11-15-19-23-27-31-35-47(57)66-40-44(69-48(58)36-32-28-24-20-16-12-6-4-3-5-9-13-17-21-25-29-33-39-56)41-67-72(62,63)71-73(64,65)68-42-45-49(59)50(60)51(70-45)55-38-37-46(53)54-52(55)61/h3,5-6,12-13,17,20,24,37-38,43-45,49-51,56,59-60H,4,7-11,14-16,18-19,21-23,25-36,39-42H2,1-2H3,(H,62,63)(H,64,65)(H2,53,54,61)/b5-3-,12-6-,17-13-,24-20-/t44-,45-,49-,50-,51-/m1/s1
InChI KeyHRNZMPZRUSUBIW-BAMXKHNKSA-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
logP6.99ALOGPS
logP10.07ChemAxon
logS-5.9ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.027ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area283.5 ŲChemAxon
Rotatable Bond Count46ChemAxon
Refractivity283.36 m³·mol⁻¹ChemAxon
Polarizability118.04 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+325.9232859911
AllCCS[M+H-H2O]+326.42232859911
AllCCS[M+Na]+325.27332859911
AllCCS[M+NH4]+325.42232859911
AllCCS[M-H]-303.59332859911
AllCCS[M+Na-2H]-310.17132859911
AllCCS[M+HCOO]-317.28432859911
DeepCCS[M+H]+295.52730932474
DeepCCS[M-H]-293.7630932474
DeepCCS[M-2H]-327.80630932474
DeepCCS[M+Na]+301.5730932474

Predicted Kovats Retention Indices

Not Available
Spectra
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 ]