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Showing metabocard for CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)) (HMDB0293728)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 16:41:38 UTC
Update Date2022-11-30 20:08:42 UTC
HMDB IDHMDB0293728
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(i-16:0/18:1(12Z)-2OH(9,10))
DescriptionCDP-DG(i-16:0/18:1(12Z)-2OH(9,10)) 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-16:0/18:1(12Z)-2OH(9,10)), in particular, consists of one chain of one 14-methylpentadecanoyl at the C-1 position and one chain of 9,10-hydroxy-octadecenoyl 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 HMDB0293728 (CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)))

CDP-DG(i-16:0/18:1(12Z)-2OH(9,10))
  Mrv1652309172118422D          

 69 70  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0293728 (CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)))

HMDB0293728
     RDKit          3D
CDP-DG(i-16:0/18:1(12Z)-2OH(9,10))
151152  0  0  0  0  0  0  0  0999 V2000
   -0.1112   -8.1685   -1.4706 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3569   -7.9091   -1.4692 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8839   -7.2897   -0.2150 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2664   -5.9467    0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9459   -5.4592    1.4006 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7253   -6.3891    2.5251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6371   -7.0571    3.1922 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.1464    9.0653   -1.5485 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2235    7.7891   -1.6442 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0122    6.8124   -2.1629 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1731    6.6005   -1.7194 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1990    3.7431   -2.9616 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1621    3.6865   -1.9575 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5385    2.7224   -4.0286 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9209    2.8318   -4.2462 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0293728 (CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)))

CDP-DG(i-16:0/18:1(12Z)-2OH(9,10))
  Mrv1652309172118422D          

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 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 46 48  1  0  0  0  0
 49 50  2  0  0  0  0
 49 51  1  0  0  0  0
 51 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 58 59  1  6  0  0  0
 58 60  1  0  0  0  0
 60 61  1  6  0  0  0
 60 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  2  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
 68 69  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0293728

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CCCCCCCCCCCCC(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)CCCCCCC[C@H](O)[C@@H](O)C\C=C/CCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C46H83N3O17P2/c1-4-5-6-7-16-21-26-37(50)38(51)27-22-17-14-19-24-29-42(53)64-36(32-61-41(52)28-23-18-13-11-9-8-10-12-15-20-25-35(2)3)33-62-67(57,58)66-68(59,60)63-34-39-43(54)44(55)45(65-39)49-31-30-40(47)48-46(49)56/h16,21,30-31,35-39,43-45,50-51,54-55H,4-15,17-20,22-29,32-34H2,1-3H3,(H,57,58)(H,59,60)(H2,47,48,56)/b21-16-/t36-,37+,38+,39-,43-,44-,45-/m1/s1

> <INCHI_KEY>
VENJETDXKYRLGB-NULVJXKLSA-N

> <FORMULA>
C46H83N3O17P2

> <MOLECULAR_WEIGHT>
1012.122

> <EXACT_MASS>
1011.519772221

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
151

> <JCHEM_AVERAGE_POLARIZABILITY>
109.4502868584819

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <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}({[(2R)-2-{[(9S,10S,12Z)-9,10-dihydroxyoctadec-12-enoyl]oxy}-3-[(14-methylpentadecanoyl)oxy]propoxy](hydroxy)phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
4.84

> <JCHEM_LOGP>
7.464793749333334

> <ALOGPS_LOGS>
-4.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
1.8631673657138115

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.0319899404417372

> <JCHEM_PKA_STRONGEST_BASIC>
3.2716255535941783

> <JCHEM_POLAR_SURFACE_AREA>
303.7300000000001

> <JCHEM_REFRACTIVITY>
253.50770000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
42

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.43e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-2-{[(9S,10S,12Z)-9,10-dihydroxyoctadec-12-enoyl]oxy}-3-[(14-methylpentadecanoyl)oxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0293728 (CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)))

HMDB0293728
     RDKit          3D
CDP-DG(i-16:0/18:1(12Z)-2OH(9,10))
151152  0  0  0  0  0  0  0  0999 V2000
   -0.1112   -8.1685   -1.4706 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3569   -7.9091   -1.4692 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8839   -7.2897   -0.2150 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2664   -5.9467    0.1077 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9459   -5.4592    1.4006 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7253   -6.3891    2.5251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6371   -7.0571    3.1922 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0573   -6.9643    2.8875 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9482   -6.4609    3.9865 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.8921   -7.2767    5.0879 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5618   -5.0864    4.3911 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3519   -5.0783    5.0313 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5933   -4.3110    5.1603 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8491   -4.1095    4.3549 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6849   -3.3905    3.0864 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3458   -1.9783    3.0156 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1897   -1.3751    3.6856 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1714    0.1095    3.2846 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8702    0.3209    1.8279 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4711   -0.0984    1.5093 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6839   -0.4745    2.4086 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9827   -0.0829    0.2105 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6601   -0.4502    0.0002 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4268   -1.6602   -0.8842 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0025   -1.8438   -0.8154 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7240   -2.8054   -1.4317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1258   -3.6314   -2.1592 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2204   -2.8403   -1.2113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9533   -2.1546   -2.2961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4294   -2.1441   -2.3153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2223   -1.5895   -1.2053 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1706   -2.3473    0.0555 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9816   -1.7198    1.1959 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4760   -0.3496    1.5160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2399    0.2555    2.6580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6986    0.4268    2.4347 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0477    1.3039    1.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5118    2.7023    1.3995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0310    3.4288    2.6188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4698    4.8363    2.6956 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0446    5.4816    3.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8829    5.6923    1.5428 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9041    0.6967   -0.6979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4107    0.3976   -0.9433 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1869    1.7086   -1.7429 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.2791    2.9064   -1.5670 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6389    2.0985   -0.9557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3917    1.2505   -3.3317 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9124    2.3548   -4.4776 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.9442    3.4809   -4.6337 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9416    1.5485   -5.9888 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6350    2.9793   -4.2444 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4449    2.7777   -5.3580 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8367    3.3427   -5.2096 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8391    4.6951   -5.0150 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2934    5.0181   -3.7673 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5077    6.0814   -3.1649 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2716    6.2975   -3.6455 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4590    7.2898   -3.1246 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9937    8.0426   -2.0841 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1464    9.0653   -1.5485 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2235    7.7891   -1.6442 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0122    6.8124   -2.1629 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1731    6.6005   -1.7194 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1990    3.7431   -2.9616 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1621    3.6865   -1.9575 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5385    2.7224   -4.0286 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9209    2.8318   -4.2462 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2836   -9.0788   -2.1184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7106   -7.3565   -1.9604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4551   -8.4136   -0.4560 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8869   -8.8946   -1.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5907   -7.3034   -2.3829 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6674   -7.9910    0.6198 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9887   -7.1986   -0.2957 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1891   -5.9973    0.2171 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5384   -5.2192   -0.6863 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3952   -4.4709    1.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9791   -5.2386    1.1404 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6569   -6.5291    2.8270 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3049   -7.7051    4.0038 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4555   -7.9942    2.5356 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2013   -6.3699    1.9444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0322   -6.4832    3.6088 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9736   -7.5359    5.3308 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3468   -4.5424    3.4009 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6528   -4.5481    4.6230 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2256   -3.3946    5.5692 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8478   -4.9694    6.0505 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3167   -5.0920    4.1801 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6250   -3.5699    4.9941 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0384   -4.0422    2.3958 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6975   -3.4964    2.5490 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2206   -1.7415    1.8969 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2438   -1.3068    3.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1996   -1.7727    3.4464 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2881   -1.3085    4.8024 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1320    0.5995    3.5105 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3063    0.5450    3.8474 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8446    1.4468    1.6933 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6169   -0.0371    1.1248 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1729   -0.6856    0.9591 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6846   -1.4608   -1.9279 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8630   -2.5783   -0.4539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4941   -3.8736   -1.0086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3484   -2.2045   -0.2909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6126   -2.6496   -3.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5797   -1.0666   -2.3582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7543   -3.2282   -2.5027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7248   -1.6566   -3.3054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0020   -0.4907   -1.0547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3039   -1.5464   -1.5830 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.7543   -2.3541    2.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0536   -1.7987    1.0271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5810    0.3709    0.6680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4055   -0.4233    1.7828 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7325    1.1940    3.0122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1186   -0.4557    3.5173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1445   -0.5731    2.2284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1262    0.8872    3.3441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1730    1.4207    1.2866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8407    0.8583    0.2791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3840    2.6966    1.4629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7505    3.3070    0.4903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7526    2.8962    3.5420 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1547    3.5247    2.5738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3637    4.8352    2.7851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6981    4.9732    4.8699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1436    5.4261    3.9027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7772    6.5559    3.9584 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1662    5.6143    0.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9362    6.7803    1.8174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9205    5.4339    1.2152 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4515    0.9691   -1.6447 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9570    1.5752   -0.0393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4193    1.6058   -1.3046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2495    0.8264   -6.0103 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5336    1.7107   -5.6332 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9665    3.2675   -6.2588 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4185    3.1366   -6.1447 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3849    5.2800   -3.8258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8656    5.7127   -4.4539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5354    7.4805   -3.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3110    9.7225   -2.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0037    9.1479   -0.5245 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1704    3.5848   -2.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1408    2.7832   -1.5831 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2217    1.7102   -3.8001 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3843    3.2975   -3.5094 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  1  0
 28 29  1  0
 29 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
 36 37  1  0
 37 38  1  0
 38 39  1  0
 39 40  1  0
 40 41  1  0
 40 42  1  0
 23 43  1  0
 43 44  1  0
 44 45  1  0
 45 46  2  0
 45 47  1  0
 45 48  1  0
 48 49  1  0
 49 50  2  0
 49 51  1  0
 49 52  1  0
 52 53  1  0
 53 54  1  0
 54 55  1  0
 55 56  1  0
 56 57  1  0
 57 58  1  0
 58 59  2  0
 59 60  1  0
 60 61  1  0
 60 62  2  0
 62 63  1  0
 63 64  2  0
 56 65  1  0
 65 66  1  0
 65 67  1  0
 67 68  1  0
 67 54  1  0
 63 57  1  0
  1 69  1  0
  1 70  1  0
  1 71  1  0
  2 72  1  0
  2 73  1  0
  3 74  1  0
  3 75  1  0
  4 76  1  0
  4 77  1  0
  5 78  1  0
  5 79  1  0
  6 80  1  0
  7 81  1  0
  8 82  1  0
  8 83  1  0
  9 84  1  6
 10 85  1  0
 11 86  1  6
 12 87  1  0
 13 88  1  0
 13 89  1  0
 14 90  1  0
 14 91  1  0
 15 92  1  0
 15 93  1  0
 16 94  1  0
 16 95  1  0
 17 96  1  0
 17 97  1  0
 18 98  1  0
 18 99  1  0
 19100  1  0
 19101  1  0
 23102  1  1
 24103  1  0
 24104  1  0
 28105  1  0
 28106  1  0
 29107  1  0
 29108  1  0
 30109  1  0
 30110  1  0
 31111  1  0
 31112  1  0
 32113  1  0
 32114  1  0
 33115  1  0
 33116  1  0
 34117  1  0
 34118  1  0
 35119  1  0
 35120  1  0
 36121  1  0
 36122  1  0
 37123  1  0
 37124  1  0
 38125  1  0
 38126  1  0
 39127  1  0
 39128  1  0
 40129  1  0
 41130  1  0
 41131  1  0
 41132  1  0
 42133  1  0
 42134  1  0
 42135  1  0
 43136  1  0
 43137  1  0
 47138  1  0
 51139  1  0
 53140  1  0
 53141  1  0
 54142  1  6
 56143  1  6
 58144  1  0
 59145  1  0
 61146  1  0
 61147  1  0
 65148  1  1
 66149  1  0
 67150  1  1
 68151  1  0
M  END
Download

PDB for HMDB0293728 (CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)))

HEADER    PROTEIN                                 17-SEP-21   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(i-16:0/18:1(12Z)-2OH(9,10))                
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     -27.085  -0.103   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -6.551  -1.383   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0      -6.551  -2.823   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      -7.884  -0.612   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -9.217  -1.383   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -10.550  -0.612   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -11.883  -1.383   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -13.216  -0.612   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0     -14.549  -1.383   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -15.882  -0.612   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -17.215  -1.383   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0     -17.215  -2.823   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0     -18.548  -0.612   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0     -18.548   0.828   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0     -19.881  -1.383   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -21.214  -0.612   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -22.754  -0.612   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -24.087  -1.383   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -25.420  -0.612   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -26.753  -1.383   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0     -28.086  -0.612   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0     -29.419  -1.383   0.000  0.00  0.00           C+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   49                                                       
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   48                                                  
CONECT   47   46                                                            
CONECT   48   46                                                            
CONECT   49    6   50   51                                                  
CONECT   50   49                                                            
CONECT   51   49   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59   60                                                  
CONECT   59   58                                                            
CONECT   60   58   61   62                                                  
CONECT   61   60                                                            
CONECT   62   60   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                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  140    0
END
Download

3D PDB for HMDB0293728 (CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)))

COMPND    HMDB0293728
HETATM    1  C1  UNL     1      -0.111  -8.168  -1.471  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.357  -7.909  -1.469  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.884  -7.290  -0.215  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.266  -5.947   0.108  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.946  -5.459   1.401  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.725  -6.389   2.525  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.637  -7.057   3.192  1.00  0.00           C  
HETATM    8  C8  UNL     1       4.057  -6.964   2.888  1.00  0.00           C  
HETATM    9  C9  UNL     1       4.948  -6.461   3.986  1.00  0.00           C  
HETATM   10  O1  UNL     1       4.892  -7.277   5.088  1.00  0.00           O  
HETATM   11  C10 UNL     1       4.562  -5.086   4.391  1.00  0.00           C  
HETATM   12  O2  UNL     1       3.352  -5.078   5.031  1.00  0.00           O  
HETATM   13  C11 UNL     1       5.593  -4.311   5.160  1.00  0.00           C  
HETATM   14  C12 UNL     1       6.849  -4.109   4.355  1.00  0.00           C  
HETATM   15  C13 UNL     1       6.685  -3.391   3.086  1.00  0.00           C  
HETATM   16  C14 UNL     1       6.346  -1.978   3.016  1.00  0.00           C  
HETATM   17  C15 UNL     1       5.190  -1.375   3.686  1.00  0.00           C  
HETATM   18  C16 UNL     1       5.171   0.110   3.285  1.00  0.00           C  
HETATM   19  C17 UNL     1       4.870   0.321   1.828  1.00  0.00           C  
HETATM   20  C18 UNL     1       3.471  -0.098   1.509  1.00  0.00           C  
HETATM   21  O3  UNL     1       2.684  -0.475   2.409  1.00  0.00           O  
HETATM   22  O4  UNL     1       2.983  -0.083   0.210  1.00  0.00           O  
HETATM   23  C19 UNL     1       1.660  -0.450   0.000  1.00  0.00           C  
HETATM   24  C20 UNL     1       1.427  -1.660  -0.884  1.00  0.00           C  
HETATM   25  O5  UNL     1       0.003  -1.844  -0.815  1.00  0.00           O  
HETATM   26  C21 UNL     1      -0.724  -2.805  -1.432  1.00  0.00           C  
HETATM   27  O6  UNL     1      -0.126  -3.631  -2.159  1.00  0.00           O  
HETATM   28  C22 UNL     1      -2.220  -2.840  -1.211  1.00  0.00           C  
HETATM   29  C23 UNL     1      -2.953  -2.155  -2.296  1.00  0.00           C  
HETATM   30  C24 UNL     1      -4.429  -2.144  -2.315  1.00  0.00           C  
HETATM   31  C25 UNL     1      -5.222  -1.590  -1.205  1.00  0.00           C  
HETATM   32  C26 UNL     1      -5.171  -2.347   0.055  1.00  0.00           C  
HETATM   33  C27 UNL     1      -5.982  -1.720   1.196  1.00  0.00           C  
HETATM   34  C28 UNL     1      -5.476  -0.350   1.516  1.00  0.00           C  
HETATM   35  C29 UNL     1      -6.240   0.256   2.658  1.00  0.00           C  
HETATM   36  C30 UNL     1      -7.699   0.427   2.435  1.00  0.00           C  
HETATM   37  C31 UNL     1      -8.048   1.304   1.282  1.00  0.00           C  
HETATM   38  C32 UNL     1      -7.512   2.702   1.399  1.00  0.00           C  
HETATM   39  C33 UNL     1      -8.031   3.429   2.619  1.00  0.00           C  
HETATM   40  C34 UNL     1      -7.470   4.836   2.696  1.00  0.00           C  
HETATM   41  C35 UNL     1      -8.045   5.482   3.951  1.00  0.00           C  
HETATM   42  C36 UNL     1      -7.883   5.692   1.543  1.00  0.00           C  
HETATM   43  C37 UNL     1       0.904   0.697  -0.698  1.00  0.00           C  
HETATM   44  O7  UNL     1      -0.411   0.398  -0.943  1.00  0.00           O  
HETATM   45  P1  UNL     1      -1.187   1.709  -1.743  1.00  0.00           P  
HETATM   46  O8  UNL     1      -0.279   2.906  -1.567  1.00  0.00           O  
HETATM   47  O9  UNL     1      -2.639   2.099  -0.956  1.00  0.00           O  
HETATM   48  O10 UNL     1      -1.392   1.251  -3.332  1.00  0.00           O  
HETATM   49  P2  UNL     1      -0.912   2.355  -4.478  1.00  0.00           P  
HETATM   50  O11 UNL     1      -1.944   3.481  -4.634  1.00  0.00           O  
HETATM   51  O12 UNL     1      -0.942   1.548  -5.989  1.00  0.00           O  
HETATM   52  O13 UNL     1       0.635   2.979  -4.244  1.00  0.00           O  
HETATM   53  C38 UNL     1       1.445   2.778  -5.358  1.00  0.00           C  
HETATM   54  C39 UNL     1       2.837   3.343  -5.210  1.00  0.00           C  
HETATM   55  O14 UNL     1       2.839   4.695  -5.015  1.00  0.00           O  
HETATM   56  C40 UNL     1       3.293   5.018  -3.767  1.00  0.00           C  
HETATM   57  N1  UNL     1       2.508   6.081  -3.165  1.00  0.00           N  
HETATM   58  C41 UNL     1       1.272   6.297  -3.645  1.00  0.00           C  
HETATM   59  C42 UNL     1       0.459   7.290  -3.125  1.00  0.00           C  
HETATM   60  C43 UNL     1       0.994   8.043  -2.084  1.00  0.00           C  
HETATM   61  N2  UNL     1       0.146   9.065  -1.549  1.00  0.00           N  
HETATM   62  N3  UNL     1       2.224   7.789  -1.644  1.00  0.00           N  
HETATM   63  C44 UNL     1       3.012   6.812  -2.163  1.00  0.00           C  
HETATM   64  O15 UNL     1       4.173   6.600  -1.719  1.00  0.00           O  
HETATM   65  C45 UNL     1       3.199   3.743  -2.962  1.00  0.00           C  
HETATM   66  O16 UNL     1       4.162   3.687  -1.957  1.00  0.00           O  
HETATM   67  C46 UNL     1       3.539   2.722  -4.029  1.00  0.00           C  
HETATM   68  O17 UNL     1       4.921   2.832  -4.246  1.00  0.00           O  
HETATM   69  H1  UNL     1      -0.284  -9.079  -2.118  1.00  0.00           H  
HETATM   70  H2  UNL     1      -0.711  -7.357  -1.960  1.00  0.00           H  
HETATM   71  H3  UNL     1      -0.455  -8.414  -0.456  1.00  0.00           H  
HETATM   72  H4  UNL     1       1.887  -8.895  -1.588  1.00  0.00           H  
HETATM   73  H5  UNL     1       1.591  -7.303  -2.383  1.00  0.00           H  
HETATM   74  H6  UNL     1       1.667  -7.991   0.620  1.00  0.00           H  
HETATM   75  H7  UNL     1       2.989  -7.199  -0.296  1.00  0.00           H  
HETATM   76  H8  UNL     1       0.189  -5.997   0.217  1.00  0.00           H  
HETATM   77  H9  UNL     1       1.538  -5.219  -0.686  1.00  0.00           H  
HETATM   78  H10 UNL     1       1.395  -4.471   1.600  1.00  0.00           H  
HETATM   79  H11 UNL     1       2.979  -5.239   1.140  1.00  0.00           H  
HETATM   80  H12 UNL     1       0.657  -6.529   2.827  1.00  0.00           H  
HETATM   81  H13 UNL     1       2.305  -7.705   4.004  1.00  0.00           H  
HETATM   82  H14 UNL     1       4.455  -7.994   2.536  1.00  0.00           H  
HETATM   83  H15 UNL     1       4.201  -6.370   1.944  1.00  0.00           H  
HETATM   84  H16 UNL     1       6.032  -6.483   3.609  1.00  0.00           H  
HETATM   85  H17 UNL     1       3.974  -7.536   5.331  1.00  0.00           H  
HETATM   86  H18 UNL     1       4.347  -4.542   3.401  1.00  0.00           H  
HETATM   87  H19 UNL     1       2.653  -4.548   4.623  1.00  0.00           H  
HETATM   88  H20 UNL     1       5.226  -3.395   5.569  1.00  0.00           H  
HETATM   89  H21 UNL     1       5.848  -4.969   6.051  1.00  0.00           H  
HETATM   90  H22 UNL     1       7.317  -5.092   4.180  1.00  0.00           H  
HETATM   91  H23 UNL     1       7.625  -3.570   4.994  1.00  0.00           H  
HETATM   92  H24 UNL     1       6.038  -4.042   2.396  1.00  0.00           H  
HETATM   93  H25 UNL     1       7.697  -3.496   2.549  1.00  0.00           H  
HETATM   94  H26 UNL     1       6.221  -1.742   1.897  1.00  0.00           H  
HETATM   95  H27 UNL     1       7.244  -1.307   3.259  1.00  0.00           H  
HETATM   96  H28 UNL     1       4.200  -1.773   3.446  1.00  0.00           H  
HETATM   97  H29 UNL     1       5.288  -1.308   4.802  1.00  0.00           H  
HETATM   98  H30 UNL     1       6.132   0.599   3.510  1.00  0.00           H  
HETATM   99  H31 UNL     1       4.306   0.545   3.847  1.00  0.00           H  
HETATM  100  H32 UNL     1       4.845   1.447   1.693  1.00  0.00           H  
HETATM  101  H33 UNL     1       5.617  -0.037   1.125  1.00  0.00           H  
HETATM  102  H34 UNL     1       1.173  -0.686   0.959  1.00  0.00           H  
HETATM  103  H35 UNL     1       1.685  -1.461  -1.928  1.00  0.00           H  
HETATM  104  H36 UNL     1       1.863  -2.578  -0.454  1.00  0.00           H  
HETATM  105  H37 UNL     1      -2.494  -3.874  -1.009  1.00  0.00           H  
HETATM  106  H38 UNL     1      -2.348  -2.205  -0.291  1.00  0.00           H  
HETATM  107  H39 UNL     1      -2.613  -2.650  -3.264  1.00  0.00           H  
HETATM  108  H40 UNL     1      -2.580  -1.067  -2.358  1.00  0.00           H  
HETATM  109  H41 UNL     1      -4.754  -3.228  -2.503  1.00  0.00           H  
HETATM  110  H42 UNL     1      -4.725  -1.657  -3.305  1.00  0.00           H  
HETATM  111  H43 UNL     1      -5.002  -0.491  -1.055  1.00  0.00           H  
HETATM  112  H44 UNL     1      -6.304  -1.546  -1.583  1.00  0.00           H  
HETATM  113  H45 UNL     1      -5.763  -3.320  -0.146  1.00  0.00           H  
HETATM  114  H46 UNL     1      -4.232  -2.651   0.468  1.00  0.00           H  
HETATM  115  H47 UNL     1      -5.754  -2.354   2.099  1.00  0.00           H  
HETATM  116  H48 UNL     1      -7.054  -1.799   1.027  1.00  0.00           H  
HETATM  117  H49 UNL     1      -5.581   0.371   0.668  1.00  0.00           H  
HETATM  118  H50 UNL     1      -4.405  -0.423   1.783  1.00  0.00           H  
HETATM  119  H51 UNL     1      -5.732   1.194   3.012  1.00  0.00           H  
HETATM  120  H52 UNL     1      -6.119  -0.456   3.517  1.00  0.00           H  
HETATM  121  H53 UNL     1      -8.145  -0.573   2.228  1.00  0.00           H  
HETATM  122  H54 UNL     1      -8.126   0.887   3.344  1.00  0.00           H  
HETATM  123  H55 UNL     1      -9.173   1.421   1.287  1.00  0.00           H  
HETATM  124  H56 UNL     1      -7.841   0.858   0.279  1.00  0.00           H  
HETATM  125  H57 UNL     1      -6.384   2.697   1.463  1.00  0.00           H  
HETATM  126  H58 UNL     1      -7.751   3.307   0.490  1.00  0.00           H  
HETATM  127  H59 UNL     1      -7.753   2.896   3.542  1.00  0.00           H  
HETATM  128  H60 UNL     1      -9.155   3.525   2.574  1.00  0.00           H  
HETATM  129  H61 UNL     1      -6.364   4.835   2.785  1.00  0.00           H  
HETATM  130  H62 UNL     1      -7.698   4.973   4.870  1.00  0.00           H  
HETATM  131  H63 UNL     1      -9.144   5.426   3.903  1.00  0.00           H  
HETATM  132  H64 UNL     1      -7.777   6.556   3.958  1.00  0.00           H  
HETATM  133  H65 UNL     1      -7.166   5.614   0.692  1.00  0.00           H  
HETATM  134  H66 UNL     1      -7.936   6.780   1.817  1.00  0.00           H  
HETATM  135  H67 UNL     1      -8.920   5.434   1.215  1.00  0.00           H  
HETATM  136  H68 UNL     1       1.451   0.969  -1.645  1.00  0.00           H  
HETATM  137  H69 UNL     1       0.957   1.575  -0.039  1.00  0.00           H  
HETATM  138  H70 UNL     1      -3.419   1.606  -1.305  1.00  0.00           H  
HETATM  139  H71 UNL     1      -0.250   0.826  -6.010  1.00  0.00           H  
HETATM  140  H72 UNL     1       1.534   1.711  -5.633  1.00  0.00           H  
HETATM  141  H73 UNL     1       0.967   3.268  -6.259  1.00  0.00           H  
HETATM  142  H74 UNL     1       3.418   3.137  -6.145  1.00  0.00           H  
HETATM  143  H75 UNL     1       4.385   5.280  -3.826  1.00  0.00           H  
HETATM  144  H76 UNL     1       0.866   5.713  -4.454  1.00  0.00           H  
HETATM  145  H77 UNL     1      -0.535   7.481  -3.494  1.00  0.00           H  
HETATM  146  H78 UNL     1      -0.311   9.722  -2.221  1.00  0.00           H  
HETATM  147  H79 UNL     1      -0.004   9.148  -0.524  1.00  0.00           H  
HETATM  148  H80 UNL     1       2.170   3.585  -2.568  1.00  0.00           H  
HETATM  149  H81 UNL     1       4.141   2.783  -1.583  1.00  0.00           H  
HETATM  150  H82 UNL     1       3.222   1.710  -3.800  1.00  0.00           H  
HETATM  151  H83 UNL     1       5.384   3.298  -3.509  1.00  0.00           H  
CONECT    1    2   69   70   71
CONECT    2    3   72   73
CONECT    3    4   74   75
CONECT    4    5   76   77
CONECT    5    6   78   79
CONECT    6    7    7   80
CONECT    7    8   81
CONECT    8    9   82   83
CONECT    9   10   11   84
CONECT   10   85
CONECT   11   12   13   86
CONECT   12   87
CONECT   13   14   88   89
CONECT   14   15   90   91
CONECT   15   16   92   93
CONECT   16   17   94   95
CONECT   17   18   96   97
CONECT   18   19   98   99
CONECT   19   20  100  101
CONECT   20   21   21   22
CONECT   22   23
CONECT   23   24   43  102
CONECT   24   25  103  104
CONECT   25   26
CONECT   26   27   27   28
CONECT   28   29  105  106
CONECT   29   30  107  108
CONECT   30   31  109  110
CONECT   31   32  111  112
CONECT   32   33  113  114
CONECT   33   34  115  116
CONECT   34   35  117  118
CONECT   35   36  119  120
CONECT   36   37  121  122
CONECT   37   38  123  124
CONECT   38   39  125  126
CONECT   39   40  127  128
CONECT   40   41   42  129
CONECT   41  130  131  132
CONECT   42  133  134  135
CONECT   43   44  136  137
CONECT   44   45
CONECT   45   46   46   47   48
CONECT   47  138
CONECT   48   49
CONECT   49   50   50   51   52
CONECT   51  139
CONECT   52   53
CONECT   53   54  140  141
CONECT   54   55   67  142
CONECT   55   56
CONECT   56   57   65  143
CONECT   57   58   63
CONECT   58   59   59  144
CONECT   59   60  145
CONECT   60   61   62   62
CONECT   61  146  147
CONECT   62   63
CONECT   63   64   64
CONECT   65   66   67  148
CONECT   66  149
CONECT   67   68  150
CONECT   68  151
END
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SMILES for HMDB0293728 (CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)))

[H][C@@](COC(=O)CCCCCCCCCCCCC(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)CCCCCCC[C@H](O)[C@@H](O)C\C=C/CCCCC
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INCHI for HMDB0293728 (CDP-DG(i-16:0/18:1(12Z)-2OH(9,10)))

InChI=1S/C46H83N3O17P2/c1-4-5-6-7-16-21-26-37(50)38(51)27-22-17-14-19-24-29-42(53)64-36(32-61-41(52)28-23-18-13-11-9-8-10-12-15-20-25-35(2)3)33-62-67(57,58)66-68(59,60)63-34-39-43(54)44(55)45(65-39)49-31-30-40(47)48-46(49)56/h16,21,30-31,35-39,43-45,50-51,54-55H,4-15,17-20,22-29,32-34H2,1-3H3,(H,57,58)(H,59,60)(H2,47,48,56)/b21-16-/t36-,37+,38+,39-,43-,44-,45-/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}({[(2R)-2-{[(9S,10S,12Z)-9,10-dihydroxyoctadec-12-enoyl]oxy}-3-[(14-methylpentadecanoyl)oxy]propoxy](hydroxy)phosphoryl}oxy)phosphinateGenerator
Chemical FormulaC46H83N3O17P2
Average Molecular Weight1012.122
Monoisotopic Molecular Weight1011.519772221
IUPAC Name{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-2-{[(9S,10S,12Z)-9,10-dihydroxyoctadec-12-enoyl]oxy}-3-[(14-methylpentadecanoyl)oxy]propoxy](hydroxy)phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-2-{[(9S,10S,12Z)-9,10-dihydroxyoctadec-12-enoyl]oxy}-3-[(14-methylpentadecanoyl)oxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCC(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)CCCCCCC[C@H](O)[C@@H](O)C\C=C/CCCCC
InChI Identifier
InChI=1S/C46H83N3O17P2/c1-4-5-6-7-16-21-26-37(50)38(51)27-22-17-14-19-24-29-42(53)64-36(32-61-41(52)28-23-18-13-11-9-8-10-12-15-20-25-35(2)3)33-62-67(57,58)66-68(59,60)63-34-39-43(54)44(55)45(65-39)49-31-30-40(47)48-46(49)56/h16,21,30-31,35-39,43-45,50-51,54-55H,4-15,17-20,22-29,32-34H2,1-3H3,(H,57,58)(H,59,60)(H2,47,48,56)/b21-16-/t36-,37+,38+,39-,43-,44-,45-/m1/s1
InChI KeyVENJETDXKYRLGB-NULVJXKLSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP4.84ALOGPS
logP7.46ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)-0.032ChemAxon
pKa (Strongest Basic)3.27ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area303.73 ŲChemAxon
Rotatable Bond Count42ChemAxon
Refractivity253.51 m³·mol⁻¹ChemAxon
Polarizability109.45 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]+309.58832859911
AllCCS[M+H-H2O]+310.06832859911
AllCCS[M+Na]+308.96432859911
AllCCS[M+NH4]+309.10832859911
AllCCS[M-H]-307.96232859911
AllCCS[M+Na-2H]-314.55332859911
AllCCS[M+HCOO]-321.73632859911
DeepCCS[M+H]+290.18330932474
DeepCCS[M-H]-288.35830932474
DeepCCS[M-2H]-322.17330932474
DeepCCS[M+Na]+295.94930932474

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 ]