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Showing metabocard for CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0) (HMDB0293466)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 14:46:22 UTC
Update Date2022-11-30 20:08:36 UTC
HMDB IDHMDB0293466
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0)
DescriptionCDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0) 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(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0), in particular, consists of one chain of one 11,12-epoxyeicosatrienoyl at the C-1 position and one chain of 12-methyltridecanoyl 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 HMDB0293466 (CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0))

CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0)
  Mrv1652309172116462D          

 68 70  0  0  1  0            999 V2000
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M  END
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3D MOL for HMDB0293466 (CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0))

HMDB0293466
     RDKit          3D
CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0)
144146  0  0  0  0  0  0  0  0999 V2000
    0.9536    6.7413   -4.8989 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7466    6.4732   -3.6059 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1065    5.9799   -3.9632 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9334    5.7186   -2.7470 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2882    4.6691   -1.8821 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1706    4.4193   -0.7104 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0293466 (CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0))

CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0)
  Mrv1652309172116462D          

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 66 68  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0293466

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CCC\C=C/C\C=C/CC1OC1C\C=C/CCCCC)(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)CCCCCCCCCCC(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C46H77N3O16P2/c1-4-5-6-7-16-21-26-37-38(63-37)27-22-17-12-10-14-18-23-28-41(50)59-32-36(62-42(51)29-24-19-13-9-8-11-15-20-25-35(2)3)33-60-66(55,56)65-67(57,58)61-34-39-43(52)44(53)45(64-39)49-31-30-40(47)48-46(49)54/h10,14,16-17,21-22,30-31,35-39,43-45,52-53H,4-9,11-13,15,18-20,23-29,32-34H2,1-3H3,(H,55,56)(H,57,58)(H2,47,48,54)/b14-10-,21-16-,22-17-/t36-,37?,38?,39-,43-,44-,45-/m1/s1

> <INCHI_KEY>
OLUPPNASVVYAGI-UVUBOTLRSA-N

> <FORMULA>
C46H77N3O16P2

> <MOLECULAR_WEIGHT>
990.075

> <EXACT_MASS>
989.477907407

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
144

> <JCHEM_AVERAGE_POLARIZABILITY>
104.59319968585726

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <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-[(12-methyltridecanoyl)oxy]-3-{[(5Z,8Z)-10-{3-[(2Z)-oct-2-en-1-yl]oxiran-2-yl}deca-5,8-dienoyl]oxy}propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
5.78

> <JCHEM_LOGP>
7.902654008333332

> <ALOGPS_LOGS>
-5.09

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2716255680279795

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8631677207149386

> <JCHEM_PKA_STRONGEST_BASIC>
-0.0319612918175205

> <JCHEM_POLAR_SURFACE_AREA>
275.8

> <JCHEM_REFRACTIVITY>
252.23080000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
39

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.96e-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-[(12-methyltridecanoyl)oxy]-3-{[(5Z,8Z)-10-{3-[(2Z)-oct-2-en-1-yl]oxiran-2-yl}deca-5,8-dienoyl]oxy}propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0293466 (CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0))

HMDB0293466
     RDKit          3D
CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0)
144146  0  0  0  0  0  0  0  0999 V2000
    0.9536    6.7413   -4.8989 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7466    6.4732   -3.6059 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1065    5.9799   -3.9632 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9334    5.7186   -2.7470 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2882    4.6691   -1.8821 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1706    4.4193   -0.7104 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8606    4.5837    0.5424 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5512    5.0576    1.0223 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9110    3.9942    1.9069 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6727    2.7681    1.2988 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5621    3.5198    1.6113 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0252   -3.1052    1.8225 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0047   -4.7201    0.2056 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.4062   -2.8245    4.0175 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5957   -1.8259    4.6376 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1595   -0.6047    4.7865 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4761    0.4361    5.3711 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1764    0.2200    5.8163 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4076    1.2570    6.4337 N   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3429   -2.0160    5.0723 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8418   -3.1762    4.9169 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.5589   -5.0433    4.2559 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6892   -4.3603    2.3184 C   0  0  2  0  0  0  0  0  0  0  0  0
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 65 66  1  0
 65 67  1  0
 11  9  1  0
 50 37  1  0
 46 40  1  0
  1 68  1  0
  1 69  1  0
  1 70  1  0
  2 71  1  0
  2 72  1  0
  3 73  1  0
  3 74  1  0
  4 75  1  0
  4 76  1  0
  5 77  1  0
  5 78  1  0
  6 79  1  0
  7 80  1  0
  8 81  1  0
  8 82  1  0
  9 83  1  0
 11 84  1  0
 12 85  1  0
 12 86  1  0
 13 87  1  0
 14 88  1  0
 15 89  1  0
 15 90  1  0
 16 91  1  0
 17 92  1  0
 18 93  1  0
 18 94  1  0
 19 95  1  0
 19 96  1  0
 20 97  1  0
 20 98  1  0
 24 99  1  0
 24100  1  0
 25101  1  1
 26102  1  0
 26103  1  0
 30104  1  0
 34105  1  0
 36106  1  0
 36107  1  0
 37108  1  6
 39109  1  1
 41110  1  0
 42111  1  0
 44112  1  0
 44113  1  0
 48114  1  6
 49115  1  0
 50116  1  6
 51117  1  0
 55118  1  0
 55119  1  0
 56120  1  0
 56121  1  0
 57122  1  0
 57123  1  0
 58124  1  0
 58125  1  0
 59126  1  0
 59127  1  0
 60128  1  0
 60129  1  0
 61130  1  0
 61131  1  0
 62132  1  0
 62133  1  0
 63134  1  0
 63135  1  0
 64136  1  0
 64137  1  0
 65138  1  0
 66139  1  0
 66140  1  0
 66141  1  0
 67142  1  0
 67143  1  0
 67144  1  0
M  END
Download

PDB for HMDB0293466 (CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0))

HEADER    PROTEIN                                 17-SEP-21   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0)         
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     -15.295   1.436   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -16.628   0.665   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -17.961   1.436   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -19.501   1.436   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -20.834   0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -22.167   1.436   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0     -22.167   2.876   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0     -23.500   0.665   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -24.833   1.436   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -26.166   0.665   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -27.706   0.665   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -29.039   1.436   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -30.372   0.665   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -31.705   1.436   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -33.038   0.665   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -34.371   1.436   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      -6.551  -1.383   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      -6.551  -2.823   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0      -7.884  -0.612   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -9.217  -1.383   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -10.550  -0.612   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -11.883  -1.383   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -13.216  -0.612   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -14.549  -1.383   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -15.882  -0.612   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -17.215  -1.383   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -18.548  -0.612   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -19.881  -1.383   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -21.214  -0.612   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -22.547  -1.383   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0     -22.547   0.156   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   54                                                       
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   45                                                  
CONECT   44   43   45                                                       
CONECT   45   43   44   46                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52                                                            
CONECT   54    6   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54   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   68                                                  
CONECT   67   66                                                            
CONECT   68   66                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  140    0
END
Download

3D PDB for HMDB0293466 (CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0))

COMPND    HMDB0293466
HETATM    1  C1  UNL     1       0.954   6.741  -4.899  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.747   6.473  -3.606  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.106   5.980  -3.963  1.00  0.00           C  
HETATM    4  C4  UNL     1       3.933   5.719  -2.747  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.288   4.669  -1.882  1.00  0.00           C  
HETATM    6  C6  UNL     1       4.171   4.419  -0.710  1.00  0.00           C  
HETATM    7  C7  UNL     1       3.861   4.584   0.542  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.551   5.058   1.022  1.00  0.00           C  
HETATM    9  C9  UNL     1       1.911   3.994   1.907  1.00  0.00           C  
HETATM   10  O1  UNL     1       1.673   2.768   1.299  1.00  0.00           O  
HETATM   11  C10 UNL     1       0.562   3.520   1.611  1.00  0.00           C  
HETATM   12  C11 UNL     1      -0.316   2.945   2.735  1.00  0.00           C  
HETATM   13  C12 UNL     1      -1.590   2.580   2.094  1.00  0.00           C  
HETATM   14  C13 UNL     1      -2.070   1.379   2.087  1.00  0.00           C  
HETATM   15  C14 UNL     1      -1.453   0.179   2.705  1.00  0.00           C  
HETATM   16  C15 UNL     1      -2.479  -0.345   3.676  1.00  0.00           C  
HETATM   17  C16 UNL     1      -3.006  -1.548   3.564  1.00  0.00           C  
HETATM   18  C17 UNL     1      -2.650  -2.497   2.493  1.00  0.00           C  
HETATM   19  C18 UNL     1      -2.121  -3.778   3.155  1.00  0.00           C  
HETATM   20  C19 UNL     1      -1.674  -4.773   2.073  1.00  0.00           C  
HETATM   21  C20 UNL     1      -0.524  -4.166   1.372  1.00  0.00           C  
HETATM   22  O2  UNL     1       0.025  -3.105   1.823  1.00  0.00           O  
HETATM   23  O3  UNL     1       0.005  -4.720   0.206  1.00  0.00           O  
HETATM   24  C21 UNL     1       1.128  -4.036  -0.351  1.00  0.00           C  
HETATM   25  C22 UNL     1       1.529  -4.701  -1.624  1.00  0.00           C  
HETATM   26  C23 UNL     1       2.861  -4.154  -2.100  1.00  0.00           C  
HETATM   27  O4  UNL     1       2.849  -2.825  -2.465  1.00  0.00           O  
HETATM   28  P1  UNL     1       4.396  -2.440  -3.015  1.00  0.00           P  
HETATM   29  O5  UNL     1       4.265  -2.254  -4.524  1.00  0.00           O  
HETATM   30  O6  UNL     1       5.450  -3.733  -2.700  1.00  0.00           O  
HETATM   31  O7  UNL     1       5.049  -1.060  -2.330  1.00  0.00           O  
HETATM   32  P2  UNL     1       4.401  -0.792  -0.809  1.00  0.00           P  
HETATM   33  O8  UNL     1       3.146  -1.601  -0.697  1.00  0.00           O  
HETATM   34  O9  UNL     1       3.960   0.841  -0.639  1.00  0.00           O  
HETATM   35  O10 UNL     1       5.540  -1.212   0.396  1.00  0.00           O  
HETATM   36  C24 UNL     1       5.231  -2.487   0.821  1.00  0.00           C  
HETATM   37  C25 UNL     1       6.177  -2.995   1.902  1.00  0.00           C  
HETATM   38  O11 UNL     1       6.184  -2.253   3.044  1.00  0.00           O  
HETATM   39  C26 UNL     1       5.406  -2.824   4.018  1.00  0.00           C  
HETATM   40  N1  UNL     1       4.596  -1.826   4.638  1.00  0.00           N  
HETATM   41  C27 UNL     1       5.160  -0.605   4.787  1.00  0.00           C  
HETATM   42  C28 UNL     1       4.476   0.436   5.371  1.00  0.00           C  
HETATM   43  C29 UNL     1       3.176   0.220   5.816  1.00  0.00           C  
HETATM   44  N2  UNL     1       2.408   1.257   6.434  1.00  0.00           N  
HETATM   45  N3  UNL     1       2.685  -1.014   5.635  1.00  0.00           N  
HETATM   46  C30 UNL     1       3.343  -2.016   5.072  1.00  0.00           C  
HETATM   47  O12 UNL     1       2.842  -3.176   4.917  1.00  0.00           O  
HETATM   48  C31 UNL     1       4.667  -3.969   3.391  1.00  0.00           C  
HETATM   49  O13 UNL     1       4.559  -5.043   4.256  1.00  0.00           O  
HETATM   50  C32 UNL     1       5.689  -4.360   2.318  1.00  0.00           C  
HETATM   51  O14 UNL     1       6.750  -5.063   2.878  1.00  0.00           O  
HETATM   52  O15 UNL     1       0.522  -4.654  -2.585  1.00  0.00           O  
HETATM   53  C33 UNL     1       0.028  -5.802  -3.153  1.00  0.00           C  
HETATM   54  O16 UNL     1       0.489  -6.946  -2.818  1.00  0.00           O  
HETATM   55  C34 UNL     1      -1.032  -5.811  -4.160  1.00  0.00           C  
HETATM   56  C35 UNL     1      -1.919  -4.630  -4.087  1.00  0.00           C  
HETATM   57  C36 UNL     1      -1.238  -3.345  -4.348  1.00  0.00           C  
HETATM   58  C37 UNL     1      -2.218  -2.161  -4.262  1.00  0.00           C  
HETATM   59  C38 UNL     1      -2.850  -2.103  -2.913  1.00  0.00           C  
HETATM   60  C39 UNL     1      -3.804  -0.905  -2.788  1.00  0.00           C  
HETATM   61  C40 UNL     1      -4.888  -0.969  -3.787  1.00  0.00           C  
HETATM   62  C41 UNL     1      -5.975   0.023  -3.732  1.00  0.00           C  
HETATM   63  C42 UNL     1      -5.740   1.467  -3.790  1.00  0.00           C  
HETATM   64  C43 UNL     1      -5.052   2.048  -2.601  1.00  0.00           C  
HETATM   65  C44 UNL     1      -4.862   3.562  -2.757  1.00  0.00           C  
HETATM   66  C45 UNL     1      -4.146   4.062  -1.498  1.00  0.00           C  
HETATM   67  C46 UNL     1      -6.194   4.233  -2.795  1.00  0.00           C  
HETATM   68  H1  UNL     1       0.328   5.840  -5.112  1.00  0.00           H  
HETATM   69  H2  UNL     1       0.356   7.653  -4.757  1.00  0.00           H  
HETATM   70  H3  UNL     1       1.685   6.851  -5.720  1.00  0.00           H  
HETATM   71  H4  UNL     1       1.173   5.757  -2.992  1.00  0.00           H  
HETATM   72  H5  UNL     1       1.858   7.441  -3.093  1.00  0.00           H  
HETATM   73  H6  UNL     1       3.623   6.668  -4.670  1.00  0.00           H  
HETATM   74  H7  UNL     1       2.975   4.996  -4.507  1.00  0.00           H  
HETATM   75  H8  UNL     1       4.062   6.678  -2.167  1.00  0.00           H  
HETATM   76  H9  UNL     1       4.975   5.441  -3.028  1.00  0.00           H  
HETATM   77  H10 UNL     1       3.271   3.732  -2.492  1.00  0.00           H  
HETATM   78  H11 UNL     1       2.278   4.969  -1.584  1.00  0.00           H  
HETATM   79  H12 UNL     1       5.185   4.063  -0.951  1.00  0.00           H  
HETATM   80  H13 UNL     1       4.615   4.359   1.312  1.00  0.00           H  
HETATM   81  H14 UNL     1       2.785   5.944   1.696  1.00  0.00           H  
HETATM   82  H15 UNL     1       1.871   5.447   0.276  1.00  0.00           H  
HETATM   83  H16 UNL     1       2.282   4.003   2.951  1.00  0.00           H  
HETATM   84  H17 UNL     1      -0.009   4.057   0.808  1.00  0.00           H  
HETATM   85  H18 UNL     1       0.222   2.120   3.177  1.00  0.00           H  
HETATM   86  H19 UNL     1      -0.461   3.771   3.477  1.00  0.00           H  
HETATM   87  H20 UNL     1      -2.137   3.419   1.600  1.00  0.00           H  
HETATM   88  H21 UNL     1      -3.049   1.264   1.557  1.00  0.00           H  
HETATM   89  H22 UNL     1      -0.583   0.451   3.366  1.00  0.00           H  
HETATM   90  H23 UNL     1      -1.127  -0.533   1.953  1.00  0.00           H  
HETATM   91  H24 UNL     1      -2.753   0.332   4.469  1.00  0.00           H  
HETATM   92  H25 UNL     1      -3.744  -1.801   4.340  1.00  0.00           H  
HETATM   93  H26 UNL     1      -2.020  -2.130   1.691  1.00  0.00           H  
HETATM   94  H27 UNL     1      -3.651  -2.861   2.055  1.00  0.00           H  
HETATM   95  H28 UNL     1      -2.962  -4.222   3.701  1.00  0.00           H  
HETATM   96  H29 UNL     1      -1.296  -3.561   3.845  1.00  0.00           H  
HETATM   97  H30 UNL     1      -2.496  -4.951   1.353  1.00  0.00           H  
HETATM   98  H31 UNL     1      -1.342  -5.695   2.566  1.00  0.00           H  
HETATM   99  H32 UNL     1       1.938  -4.085   0.430  1.00  0.00           H  
HETATM  100  H33 UNL     1       0.814  -2.996  -0.490  1.00  0.00           H  
HETATM  101  H34 UNL     1       1.750  -5.787  -1.407  1.00  0.00           H  
HETATM  102  H35 UNL     1       3.585  -4.332  -1.268  1.00  0.00           H  
HETATM  103  H36 UNL     1       3.154  -4.782  -2.973  1.00  0.00           H  
HETATM  104  H37 UNL     1       6.315  -3.412  -2.325  1.00  0.00           H  
HETATM  105  H38 UNL     1       4.352   1.200   0.220  1.00  0.00           H  
HETATM  106  H39 UNL     1       4.201  -2.454   1.256  1.00  0.00           H  
HETATM  107  H40 UNL     1       5.287  -3.180  -0.041  1.00  0.00           H  
HETATM  108  H41 UNL     1       7.217  -3.053   1.494  1.00  0.00           H  
HETATM  109  H42 UNL     1       6.104  -3.217   4.813  1.00  0.00           H  
HETATM  110  H43 UNL     1       6.179  -0.402   4.449  1.00  0.00           H  
HETATM  111  H44 UNL     1       4.896   1.427   5.508  1.00  0.00           H  
HETATM  112  H45 UNL     1       1.378   1.290   6.346  1.00  0.00           H  
HETATM  113  H46 UNL     1       2.880   1.988   6.977  1.00  0.00           H  
HETATM  114  H47 UNL     1       3.767  -3.694   2.851  1.00  0.00           H  
HETATM  115  H48 UNL     1       3.832  -5.666   4.060  1.00  0.00           H  
HETATM  116  H49 UNL     1       5.201  -4.903   1.490  1.00  0.00           H  
HETATM  117  H50 UNL     1       6.723  -6.028   2.625  1.00  0.00           H  
HETATM  118  H51 UNL     1      -0.583  -5.847  -5.192  1.00  0.00           H  
HETATM  119  H52 UNL     1      -1.650  -6.742  -4.046  1.00  0.00           H  
HETATM  120  H53 UNL     1      -2.359  -4.630  -3.040  1.00  0.00           H  
HETATM  121  H54 UNL     1      -2.763  -4.789  -4.822  1.00  0.00           H  
HETATM  122  H55 UNL     1      -0.378  -3.120  -3.742  1.00  0.00           H  
HETATM  123  H56 UNL     1      -0.901  -3.357  -5.427  1.00  0.00           H  
HETATM  124  H57 UNL     1      -2.943  -2.288  -5.082  1.00  0.00           H  
HETATM  125  H58 UNL     1      -1.624  -1.252  -4.467  1.00  0.00           H  
HETATM  126  H59 UNL     1      -3.501  -2.992  -2.715  1.00  0.00           H  
HETATM  127  H60 UNL     1      -2.129  -2.032  -2.086  1.00  0.00           H  
HETATM  128  H61 UNL     1      -4.186  -0.759  -1.782  1.00  0.00           H  
HETATM  129  H62 UNL     1      -3.138  -0.018  -3.053  1.00  0.00           H  
HETATM  130  H63 UNL     1      -5.397  -1.990  -3.751  1.00  0.00           H  
HETATM  131  H64 UNL     1      -4.446  -1.004  -4.853  1.00  0.00           H  
HETATM  132  H65 UNL     1      -6.684  -0.219  -4.604  1.00  0.00           H  
HETATM  133  H66 UNL     1      -6.578  -0.248  -2.788  1.00  0.00           H  
HETATM  134  H67 UNL     1      -6.696   2.047  -4.019  1.00  0.00           H  
HETATM  135  H68 UNL     1      -5.060   1.652  -4.685  1.00  0.00           H  
HETATM  136  H69 UNL     1      -4.130   1.633  -2.258  1.00  0.00           H  
HETATM  137  H70 UNL     1      -5.799   1.936  -1.742  1.00  0.00           H  
HETATM  138  H71 UNL     1      -4.260   3.768  -3.651  1.00  0.00           H  
HETATM  139  H72 UNL     1      -4.292   5.132  -1.366  1.00  0.00           H  
HETATM  140  H73 UNL     1      -3.095   3.730  -1.518  1.00  0.00           H  
HETATM  141  H74 UNL     1      -4.642   3.531  -0.652  1.00  0.00           H  
HETATM  142  H75 UNL     1      -6.972   3.554  -2.347  1.00  0.00           H  
HETATM  143  H76 UNL     1      -6.182   5.188  -2.219  1.00  0.00           H  
HETATM  144  H77 UNL     1      -6.492   4.414  -3.853  1.00  0.00           H  
CONECT    1    2   68   69   70
CONECT    2    3   71   72
CONECT    3    4   73   74
CONECT    4    5   75   76
CONECT    5    6   77   78
CONECT    6    7    7   79
CONECT    7    8   80
CONECT    8    9   81   82
CONECT    9   10   11   83
CONECT   10   11
CONECT   11   12   84
CONECT   12   13   85   86
CONECT   13   14   14   87
CONECT   14   15   88
CONECT   15   16   89   90
CONECT   16   17   17   91
CONECT   17   18   92
CONECT   18   19   93   94
CONECT   19   20   95   96
CONECT   20   21   97   98
CONECT   21   22   22   23
CONECT   23   24
CONECT   24   25   99  100
CONECT   25   26   52  101
CONECT   26   27  102  103
CONECT   27   28
CONECT   28   29   29   30   31
CONECT   30  104
CONECT   31   32
CONECT   32   33   33   34   35
CONECT   34  105
CONECT   35   36
CONECT   36   37  106  107
CONECT   37   38   50  108
CONECT   38   39
CONECT   39   40   48  109
CONECT   40   41   46
CONECT   41   42   42  110
CONECT   42   43  111
CONECT   43   44   45   45
CONECT   44  112  113
CONECT   45   46
CONECT   46   47   47
CONECT   48   49   50  114
CONECT   49  115
CONECT   50   51  116
CONECT   51  117
CONECT   52   53
CONECT   53   54   54   55
CONECT   55   56  118  119
CONECT   56   57  120  121
CONECT   57   58  122  123
CONECT   58   59  124  125
CONECT   59   60  126  127
CONECT   60   61  128  129
CONECT   61   62  130  131
CONECT   62   63  132  133
CONECT   63   64  134  135
CONECT   64   65  136  137
CONECT   65   66   67  138
CONECT   66  139  140  141
CONECT   67  142  143  144
END
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SMILES for HMDB0293466 (CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0))

[H][C@@](COC(=O)CCC\C=C/C\C=C/CC1OC1C\C=C/CCCCC)(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)CCCCCCCCCCC(C)C
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INCHI for HMDB0293466 (CDP-DG(20:3(5Z,8Z,14Z)-O(11S,12R)/i-14:0))

InChI=1S/C46H77N3O16P2/c1-4-5-6-7-16-21-26-37-38(63-37)27-22-17-12-10-14-18-23-28-41(50)59-32-36(62-42(51)29-24-19-13-9-8-11-15-20-25-35(2)3)33-60-66(55,56)65-67(57,58)61-34-39-43(52)44(53)45(64-39)49-31-30-40(47)48-46(49)54/h10,14,16-17,21-22,30-31,35-39,43-45,52-53H,4-9,11-13,15,18-20,23-29,32-34H2,1-3H3,(H,55,56)(H,57,58)(H2,47,48,54)/b14-10-,21-16-,22-17-/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}({hydroxy[(2R)-2-[(12-methyltridecanoyl)oxy]-3-{[(5Z,8Z)-10-{3-[(2Z)-oct-2-en-1-yl]oxiran-2-yl}deca-5,8-dienoyl]oxy}propoxy]phosphoryl}oxy)phosphinateGenerator
Chemical FormulaC46H77N3O16P2
Average Molecular Weight990.075
Monoisotopic Molecular Weight989.477907407
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-[(12-methyltridecanoyl)oxy]-3-{[(5Z,8Z)-10-{3-[(2Z)-oct-2-en-1-yl]oxiran-2-yl}deca-5,8-dienoyl]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-[(12-methyltridecanoyl)oxy]-3-{[(5Z,8Z)-10-{3-[(2Z)-oct-2-en-1-yl]oxiran-2-yl}deca-5,8-dienoyl]oxy}propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCC\C=C/C\C=C/CC1OC1C\C=C/CCCCC)(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)CCCCCCCCCCC(C)C
InChI Identifier
InChI=1S/C46H77N3O16P2/c1-4-5-6-7-16-21-26-37-38(63-37)27-22-17-12-10-14-18-23-28-41(50)59-32-36(62-42(51)29-24-19-13-9-8-11-15-20-25-35(2)3)33-60-66(55,56)65-67(57,58)61-34-39-43(52)44(53)45(64-39)49-31-30-40(47)48-46(49)54/h10,14,16-17,21-22,30-31,35-39,43-45,52-53H,4-9,11-13,15,18-20,23-29,32-34H2,1-3H3,(H,55,56)(H,57,58)(H2,47,48,54)/b14-10-,21-16-,22-17-/t36-,37?,38?,39-,43-,44-,45-/m1/s1
InChI KeyOLUPPNASVVYAGI-UVUBOTLRSA-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
logP5.78ALOGPS
logP7.9ChemAxon
logS-5.1ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.032ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area275.8 ŲChemAxon
Rotatable Bond Count39ChemAxon
Refractivity252.23 m³·mol⁻¹ChemAxon
Polarizability104.59 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+297.67832859911
AllCCS[M+H-H2O]+298.03332859911
AllCCS[M+Na]+297.20332859911
AllCCS[M+NH4]+297.31432859911
AllCCS[M-H]-287.11932859911
AllCCS[M+Na-2H]-294.11432859911
AllCCS[M+HCOO]-301.7332859911
DeepCCS[M+H]+242.66830932474
DeepCCS[M-H]-240.91330932474
DeepCCS[M-2H]-274.94730932474
DeepCCS[M+Na]+249.52130932474

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 ]