Hmdb loader

Showing metabocard for CDP-DG(18:2(9Z,11Z)/i-12:0) (HMDB0116052)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 06:50:25 UTC
Update Date2022-11-30 19:26:27 UTC
HMDB IDHMDB0116052
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(18:2(9Z,11Z)/i-12:0)
DescriptionCDP-DG(18:2(9Z,11Z)/i-12:0) is a cytidine diphosphate diacylglycerol or CDP-diacylglycerol (CDP-DG). CDP-diacylglycerol is an important branchpoint intermediate in eukaryotic phospholipid biosynthesis and could be a key regulatory molecule in phospholipid metabolism. It is a glycerophospholipid in which a cytidine diphosphate moiety occupies a glycerol substitution site. As is the case with diacylglycerols, CDP-diacylglycerols can have many different combinations of fatty acids of varying lengths and saturation attached at the C-1 and C-2 positions. Fatty acids containing 16, 18 and 20 carbons are the most common. CDP-DG(18:2(9Z,11Z)/i-12:0), in particular, consists of one chain of (9Z,11Z)-octadecadienoic acid at the C-1 position and one chain of isododecanoic acid at the C-2 position. Cytidine diphosphate diacylglycerols are rarely noticed in analyses of lipid compositions of tissues, as they are present is such small amounts (perhaps only 0.05% or so of the total phospholipids).
Structure
Data?1563873667
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116052 (CDP-DG(18:2(9Z,11Z)/i-12:0))

CDP-DG(18:2(9Z,11Z)/i-12:0)
  Mrv1652309161722242D          

 63 64  0  0  1  0            999 V2000
   17.4451   -4.0157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4838   -4.5706    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.5226   -4.0157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4061   -4.5706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5612   -4.5706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7337   -5.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3206   -5.7230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.4768   -4.2072    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0116052 (CDP-DG(18:2(9Z,11Z)/i-12:0))

HMDB0116052
     RDKit          3D
CDP-DG(18:2(9Z,11Z)/i-12:0)
135136  0  0  0  0  0  0  0  0999 V2000
   -0.0843   -8.8951   -1.7578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4357   -8.2726   -1.9557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2783   -8.3885   -0.7052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6296   -7.7846   -0.8537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6433   -6.3182   -1.1863 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9387   -5.5707   -0.0694 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.0898   -0.0283    3.5580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0477   -9.9359   -2.1906 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7309   -8.3238   -2.2394 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1874   -8.9715   -0.6698 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.1828   -1.3963    0.2974 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8249   -1.7984   -2.7359 H   0  0  0  0  0  0  0  0  0  0  0  0
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 62135  1  0
M  END
Download

3D SDF for HMDB0116052 (CDP-DG(18:2(9Z,11Z)/i-12:0))

CDP-DG(18:2(9Z,11Z)/i-12:0)
  Mrv1652309161722242D          

 63 64  0  0  1  0            999 V2000
   17.4451   -4.0157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4838   -4.5706    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.5226   -4.0157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4061   -4.5706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5612   -4.5706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7337   -5.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3206   -5.7230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.4768   -4.2072    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   19.4768   -5.3368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.8027   -4.5411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   21.8732   -4.1777    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
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   25.1589   -6.7486    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   24.1017   -5.0357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.4120   -3.3822    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   28.4120   -4.2072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.6975   -2.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.6975   -4.6197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.9830   -3.3822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9830   -4.2072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.6976   -2.1447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   29.1119   -4.5018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8468   -4.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8468   -3.3867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.3413   -4.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   15.0193   -6.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.8779   -5.2681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
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  4  1  1  0  0  0  0
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  8  4  1  0  0  0  0
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  8 10  1  0  0  0  0
  8 11  2  0  0  0  0
 12 10  1  0  0  0  0
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 14 23  1  0  0  0  0
 16 17  1  0  0  0  0
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 18 19  1  0  0  0  0
 18 17  1  0  0  0  0
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 32  5  1  0  0  0  0
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 61 62  1  0  0  0  0
 61 63  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0116052

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CCCCCCC\C=C/C=C\CCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCC(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C42H73N3O15P2/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-20-23-26-37(46)55-30-34(58-38(47)27-24-21-18-17-19-22-25-33(2)3)31-56-61(51,52)60-62(53,54)57-32-35-39(48)40(49)41(59-35)45-29-28-36(43)44-42(45)50/h9-12,28-29,33-35,39-41,48-49H,4-8,13-27,30-32H2,1-3H3,(H,51,52)(H,53,54)(H2,43,44,50)/b10-9-,12-11-/t34-,35-,39+,40?,41-/m1/s1

> <INCHI_KEY>
AGPRHJMUWDCGEI-JEZDYYCXSA-N

> <FORMULA>
C42H73N3O15P2

> <MOLECULAR_WEIGHT>
922.0

> <EXACT_MASS>
921.451692659

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
135

> <JCHEM_AVERAGE_POLARIZABILITY>
98.23019992634705

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-2-[(10-methylundecanoyl)oxy]-3-[(9Z,11Z)-octadeca-9,11-dienoyloxy]propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
5.47

> <JCHEM_LOGP>
7.786219566666668

> <ALOGPS_LOGS>
-4.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2716255536258676

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8631673662376511

> <JCHEM_PKA_STRONGEST_BASIC>
-0.03198989821723941

> <JCHEM_POLAR_SURFACE_AREA>
263.27

> <JCHEM_REFRACTIVITY>
233.18930000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
37

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.17e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-2-[(10-methylundecanoyl)oxy]-3-[(9Z,11Z)-octadeca-9,11-dienoyloxy]propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116052 (CDP-DG(18:2(9Z,11Z)/i-12:0))

HMDB0116052
     RDKit          3D
CDP-DG(18:2(9Z,11Z)/i-12:0)
135136  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

PDB for HMDB0116052 (CDP-DG(18:2(9Z,11Z)/i-12:0))

HEADER    PROTEIN                                 16-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(18:2(9Z,11Z)/i-12:0)                       
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-SEP-17         0                                  
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HETATM   25  C   UNK     0      53.036  -7.853   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      51.702  -5.543   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      51.702  -8.624   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      50.368  -6.313   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      50.368  -7.853   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      51.702  -4.003   0.000  0.00  0.00           N+0
HETATM   31  O   UNK     0      54.342  -8.403   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      25.847  -7.762   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      25.847  -6.322   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      24.514  -8.533   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      23.181  -7.762   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      21.848  -8.533   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      20.515  -7.762   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      19.182  -8.533   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      17.849  -7.762   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      16.516  -8.533   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      15.183  -7.762   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      13.643  -7.762   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      12.310  -8.533   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      10.770  -8.533   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       9.437  -7.762   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       8.104  -8.533   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       6.771  -7.762   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       5.438  -8.533   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       4.105  -7.762   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       2.771  -8.533   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      28.036 -11.374   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      28.036 -12.814   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0      26.703 -10.603   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      25.370 -11.374   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      24.037 -10.603   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      22.704 -11.374   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      21.371 -10.603   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      20.038 -11.374   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      18.705 -10.603   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      17.372 -11.374   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      16.038 -10.603   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      14.705 -11.374   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      14.705  -9.834   0.000  0.00  0.00           C+0
CONECT    1    2    4                                                       
CONECT    2    1    6    7    3                                             
CONECT    3    2    5                                                       
CONECT    4    1    8                                                       
CONECT    5    3   32                                                       
CONECT    6    2   51                                                       
CONECT    7    2                                                            
CONECT    8    4    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8   12                                                       
CONECT   11    8                                                            
CONECT   12   10   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12   23                                                       
CONECT   15   12                                                            
CONECT   16   17   22   20                                                  
CONECT   17   16   18   21                                                  
CONECT   18   19   17   27                                                  
CONECT   19   18   20                                                       
CONECT   20   19   16   23                                                  
CONECT   21   17                                                            
CONECT   22   16                                                            
CONECT   23   14   20                                                       
CONECT   24   25   26                                                       
CONECT   25   24   27   31                                                  
CONECT   26   24   28   30                                                  
CONECT   27   18   25   29                                                  
CONECT   28   26   29                                                       
CONECT   29   27   28                                                       
CONECT   30   26                                                            
CONECT   31   25                                                            
CONECT   32    5   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                                                            
CONECT   51    6   52   53                                                  
CONECT   52   51                                                            
CONECT   53   51   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62   63                                                  
CONECT   62   61                                                            
CONECT   63   61                                                            
MASTER        0    0    0    0    0    0    0    0   63    0  128    0
END
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3D PDB for HMDB0116052 (CDP-DG(18:2(9Z,11Z)/i-12:0))

COMPND    HMDB0116052
HETATM    1  C1  UNL     1      -0.084  -8.895  -1.758  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.436  -8.273  -1.956  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.278  -8.388  -0.705  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.630  -7.785  -0.854  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.643  -6.318  -1.186  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.939  -5.571  -0.069  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.897  -4.137  -0.277  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.777  -3.445  -0.376  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.466  -4.014  -0.295  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.650  -3.332  -0.390  1.00  0.00           C  
HETATM   11  C11 UNL     1       0.686  -1.895  -0.592  1.00  0.00           C  
HETATM   12  C12 UNL     1       1.399  -1.485  -1.869  1.00  0.00           C  
HETATM   13  C13 UNL     1       2.814  -1.933  -1.912  1.00  0.00           C  
HETATM   14  C14 UNL     1       3.455  -1.500  -3.202  1.00  0.00           C  
HETATM   15  C15 UNL     1       3.448   0.008  -3.344  1.00  0.00           C  
HETATM   16  C16 UNL     1       4.111   0.332  -4.641  1.00  0.00           C  
HETATM   17  C17 UNL     1       4.222   1.770  -4.989  1.00  0.00           C  
HETATM   18  C18 UNL     1       2.974   2.513  -5.122  1.00  0.00           C  
HETATM   19  O1  UNL     1       2.946   3.456  -5.989  1.00  0.00           O  
HETATM   20  O2  UNL     1       1.801   2.330  -4.427  1.00  0.00           O  
HETATM   21  C19 UNL     1       0.664   3.126  -4.675  1.00  0.00           C  
HETATM   22  C20 UNL     1      -0.504   2.751  -3.774  1.00  0.00           C  
HETATM   23  C21 UNL     1      -0.336   3.258  -2.387  1.00  0.00           C  
HETATM   24  O3  UNL     1       0.627   2.646  -1.621  1.00  0.00           O  
HETATM   25  P1  UNL     1       0.583   3.448  -0.107  1.00  0.00           P  
HETATM   26  O4  UNL     1      -0.608   2.896   0.638  1.00  0.00           O  
HETATM   27  O5  UNL     1       0.318   5.114  -0.374  1.00  0.00           O  
HETATM   28  O6  UNL     1       1.937   3.164   0.811  1.00  0.00           O  
HETATM   29  P2  UNL     1       3.390   3.282  -0.003  1.00  0.00           P  
HETATM   30  O7  UNL     1       3.227   2.832  -1.432  1.00  0.00           O  
HETATM   31  O8  UNL     1       4.016   4.848  -0.033  1.00  0.00           O  
HETATM   32  O9  UNL     1       4.521   2.292   0.785  1.00  0.00           O  
HETATM   33  C22 UNL     1       4.571   2.625   2.155  1.00  0.00           C  
HETATM   34  C23 UNL     1       5.555   1.752   2.898  1.00  0.00           C  
HETATM   35  O10 UNL     1       5.597   2.093   4.244  1.00  0.00           O  
HETATM   36  C24 UNL     1       4.440   1.586   4.825  1.00  0.00           C  
HETATM   37  N1  UNL     1       3.499   2.630   5.128  1.00  0.00           N  
HETATM   38  C25 UNL     1       2.164   2.491   5.133  1.00  0.00           C  
HETATM   39  C26 UNL     1       1.323   3.550   5.436  1.00  0.00           C  
HETATM   40  C27 UNL     1       1.849   4.795   5.745  1.00  0.00           C  
HETATM   41  N2  UNL     1       0.982   5.873   6.053  1.00  0.00           N  
HETATM   42  N3  UNL     1       3.191   4.888   5.728  1.00  0.00           N  
HETATM   43  C28 UNL     1       3.996   3.851   5.432  1.00  0.00           C  
HETATM   44  O11 UNL     1       5.249   4.033   5.441  1.00  0.00           O  
HETATM   45  C29 UNL     1       3.901   0.507   3.959  1.00  0.00           C  
HETATM   46  O12 UNL     1       3.625  -0.663   4.664  1.00  0.00           O  
HETATM   47  C30 UNL     1       5.024   0.312   2.959  1.00  0.00           C  
HETATM   48  O13 UNL     1       4.566  -0.100   1.721  1.00  0.00           O  
HETATM   49  O14 UNL     1      -0.860   1.417  -3.900  1.00  0.00           O  
HETATM   50  C31 UNL     1      -2.042   1.030  -4.485  1.00  0.00           C  
HETATM   51  O15 UNL     1      -2.826   1.945  -4.915  1.00  0.00           O  
HETATM   52  C32 UNL     1      -2.383  -0.389  -4.612  1.00  0.00           C  
HETATM   53  C33 UNL     1      -2.721  -1.166  -3.413  1.00  0.00           C  
HETATM   54  C34 UNL     1      -3.891  -0.780  -2.594  1.00  0.00           C  
HETATM   55  C35 UNL     1      -3.870   0.558  -1.925  1.00  0.00           C  
HETATM   56  C36 UNL     1      -5.195   0.659  -1.155  1.00  0.00           C  
HETATM   57  C37 UNL     1      -5.299   1.966  -0.423  1.00  0.00           C  
HETATM   58  C38 UNL     1      -4.174   2.127   0.590  1.00  0.00           C  
HETATM   59  C39 UNL     1      -4.251   0.999   1.599  1.00  0.00           C  
HETATM   60  C40 UNL     1      -3.130   1.151   2.616  1.00  0.00           C  
HETATM   61  C41 UNL     1      -3.291   2.467   3.312  1.00  0.00           C  
HETATM   62  C42 UNL     1      -3.090  -0.028   3.558  1.00  0.00           C  
HETATM   63  H1  UNL     1      -0.048  -9.936  -2.191  1.00  0.00           H  
HETATM   64  H2  UNL     1       0.731  -8.324  -2.239  1.00  0.00           H  
HETATM   65  H3  UNL     1       0.187  -8.971  -0.670  1.00  0.00           H  
HETATM   66  H4  UNL     1      -1.322  -7.243  -2.305  1.00  0.00           H  
HETATM   67  H5  UNL     1      -1.947  -8.851  -2.762  1.00  0.00           H  
HETATM   68  H6  UNL     1      -1.736  -8.042   0.171  1.00  0.00           H  
HETATM   69  H7  UNL     1      -2.435  -9.489  -0.547  1.00  0.00           H  
HETATM   70  H8  UNL     1      -4.241  -8.386  -1.561  1.00  0.00           H  
HETATM   71  H9  UNL     1      -4.143  -7.891   0.140  1.00  0.00           H  
HETATM   72  H10 UNL     1      -3.121  -6.194  -2.156  1.00  0.00           H  
HETATM   73  H11 UNL     1      -4.669  -5.974  -1.322  1.00  0.00           H  
HETATM   74  H12 UNL     1      -1.980  -6.043   0.142  1.00  0.00           H  
HETATM   75  H13 UNL     1      -3.569  -5.815   0.851  1.00  0.00           H  
HETATM   76  H14 UNL     1      -3.825  -3.591  -0.357  1.00  0.00           H  
HETATM   77  H15 UNL     1      -1.872  -2.359  -0.533  1.00  0.00           H  
HETATM   78  H16 UNL     1      -0.329  -5.117  -0.142  1.00  0.00           H  
HETATM   79  H17 UNL     1       1.611  -3.918  -0.308  1.00  0.00           H  
HETATM   80  H18 UNL     1      -0.303  -1.451  -0.639  1.00  0.00           H  
HETATM   81  H19 UNL     1       1.183  -1.396   0.297  1.00  0.00           H  
HETATM   82  H20 UNL     1       0.825  -1.798  -2.736  1.00  0.00           H  
HETATM   83  H21 UNL     1       1.388  -0.359  -1.839  1.00  0.00           H  
HETATM   84  H22 UNL     1       3.418  -1.430  -1.098  1.00  0.00           H  
HETATM   85  H23 UNL     1       2.951  -3.015  -1.713  1.00  0.00           H  
HETATM   86  H24 UNL     1       4.500  -1.864  -3.298  1.00  0.00           H  
HETATM   87  H25 UNL     1       2.822  -1.913  -4.040  1.00  0.00           H  
HETATM   88  H26 UNL     1       2.437   0.415  -3.329  1.00  0.00           H  
HETATM   89  H27 UNL     1       4.013   0.433  -2.467  1.00  0.00           H  
HETATM   90  H28 UNL     1       5.140  -0.091  -4.617  1.00  0.00           H  
HETATM   91  H29 UNL     1       3.567  -0.194  -5.457  1.00  0.00           H  
HETATM   92  H30 UNL     1       4.880   2.302  -4.257  1.00  0.00           H  
HETATM   93  H31 UNL     1       4.784   1.818  -5.966  1.00  0.00           H  
HETATM   94  H32 UNL     1       0.860   4.207  -4.494  1.00  0.00           H  
HETATM   95  H33 UNL     1       0.314   3.044  -5.727  1.00  0.00           H  
HETATM   96  H34 UNL     1      -1.363   3.363  -4.213  1.00  0.00           H  
HETATM   97  H35 UNL     1      -0.140   4.352  -2.454  1.00  0.00           H  
HETATM   98  H36 UNL     1      -1.304   3.126  -1.838  1.00  0.00           H  
HETATM   99  H37 UNL     1      -0.664   5.212  -0.525  1.00  0.00           H  
HETATM  100  H38 UNL     1       3.445   5.455   0.499  1.00  0.00           H  
HETATM  101  H39 UNL     1       5.015   3.662   2.169  1.00  0.00           H  
HETATM  102  H40 UNL     1       3.567   2.626   2.604  1.00  0.00           H  
HETATM  103  H41 UNL     1       6.547   1.803   2.446  1.00  0.00           H  
HETATM  104  H42 UNL     1       4.739   1.133   5.798  1.00  0.00           H  
HETATM  105  H43 UNL     1       1.785   1.506   4.888  1.00  0.00           H  
HETATM  106  H44 UNL     1       0.238   3.383   5.426  1.00  0.00           H  
HETATM  107  H45 UNL     1       1.188   6.881   5.892  1.00  0.00           H  
HETATM  108  H46 UNL     1       0.059   5.640   6.478  1.00  0.00           H  
HETATM  109  H47 UNL     1       3.007   0.816   3.343  1.00  0.00           H  
HETATM  110  H48 UNL     1       2.702  -0.919   4.476  1.00  0.00           H  
HETATM  111  H49 UNL     1       5.832  -0.319   3.362  1.00  0.00           H  
HETATM  112  H50 UNL     1       5.337  -0.107   1.112  1.00  0.00           H  
HETATM  113  H51 UNL     1      -3.245  -0.509  -5.343  1.00  0.00           H  
HETATM  114  H52 UNL     1      -1.515  -0.881  -5.167  1.00  0.00           H  
HETATM  115  H53 UNL     1      -1.837  -1.277  -2.708  1.00  0.00           H  
HETATM  116  H54 UNL     1      -2.915  -2.240  -3.743  1.00  0.00           H  
HETATM  117  H55 UNL     1      -4.031  -1.576  -1.812  1.00  0.00           H  
HETATM  118  H56 UNL     1      -4.837  -0.871  -3.215  1.00  0.00           H  
HETATM  119  H57 UNL     1      -3.025   0.652  -1.212  1.00  0.00           H  
HETATM  120  H58 UNL     1      -3.839   1.415  -2.587  1.00  0.00           H  
HETATM  121  H59 UNL     1      -5.979   0.691  -1.965  1.00  0.00           H  
HETATM  122  H60 UNL     1      -5.350  -0.233  -0.530  1.00  0.00           H  
HETATM  123  H61 UNL     1      -5.266   2.777  -1.167  1.00  0.00           H  
HETATM  124  H62 UNL     1      -6.241   2.049   0.146  1.00  0.00           H  
HETATM  125  H63 UNL     1      -4.392   3.072   1.149  1.00  0.00           H  
HETATM  126  H64 UNL     1      -3.192   2.193   0.102  1.00  0.00           H  
HETATM  127  H65 UNL     1      -5.244   1.034   2.095  1.00  0.00           H  
HETATM  128  H66 UNL     1      -4.172   0.002   1.110  1.00  0.00           H  
HETATM  129  H67 UNL     1      -2.188   1.134   2.012  1.00  0.00           H  
HETATM  130  H68 UNL     1      -2.687   3.226   2.756  1.00  0.00           H  
HETATM  131  H69 UNL     1      -4.353   2.802   3.305  1.00  0.00           H  
HETATM  132  H70 UNL     1      -2.956   2.373   4.378  1.00  0.00           H  
HETATM  133  H71 UNL     1      -3.812  -0.820   3.261  1.00  0.00           H  
HETATM  134  H72 UNL     1      -3.232   0.298   4.612  1.00  0.00           H  
HETATM  135  H73 UNL     1      -2.089  -0.514   3.531  1.00  0.00           H  
CONECT    1    2   63   64   65
CONECT    2    3   66   67
CONECT    3    4   68   69
CONECT    4    5   70   71
CONECT    5    6   72   73
CONECT    6    7   74   75
CONECT    7    8    8   76
CONECT    8    9   77
CONECT    9   10   10   78
CONECT   10   11   79
CONECT   11   12   80   81
CONECT   12   13   82   83
CONECT   13   14   84   85
CONECT   14   15   86   87
CONECT   15   16   88   89
CONECT   16   17   90   91
CONECT   17   18   92   93
CONECT   18   19   19   20
CONECT   20   21
CONECT   21   22   94   95
CONECT   22   23   49   96
CONECT   23   24   97   98
CONECT   24   25
CONECT   25   26   26   27   28
CONECT   27   99
CONECT   28   29
CONECT   29   30   30   31   32
CONECT   31  100
CONECT   32   33
CONECT   33   34  101  102
CONECT   34   35   47  103
CONECT   35   36
CONECT   36   37   45  104
CONECT   37   38   43
CONECT   38   39   39  105
CONECT   39   40  106
CONECT   40   41   42   42
CONECT   41  107  108
CONECT   42   43
CONECT   43   44   44
CONECT   45   46   47  109
CONECT   46  110
CONECT   47   48  111
CONECT   48  112
CONECT   49   50
CONECT   50   51   51   52
CONECT   52   53  113  114
CONECT   53   54  115  116
CONECT   54   55  117  118
CONECT   55   56  119  120
CONECT   56   57  121  122
CONECT   57   58  123  124
CONECT   58   59  125  126
CONECT   59   60  127  128
CONECT   60   61   62  129
CONECT   61  130  131  132
CONECT   62  133  134  135
END
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SMILES for HMDB0116052 (CDP-DG(18:2(9Z,11Z)/i-12:0))

[H][C@@](COC(=O)CCCCCCC\C=C/C=C\CCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCC(C)C
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INCHI for HMDB0116052 (CDP-DG(18:2(9Z,11Z)/i-12:0))

InChI=1S/C42H73N3O15P2/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-20-23-26-37(46)55-30-34(58-38(47)27-24-21-18-17-19-22-25-33(2)3)31-56-61(51,52)60-62(53,54)57-32-35-39(48)40(49)41(59-35)45-29-28-36(43)44-42(45)50/h9-12,28-29,33-35,39-41,48-49H,4-8,13-27,30-32H2,1-3H3,(H,51,52)(H,53,54)(H2,43,44,50)/b10-9-,12-11-/t34-,35-,39+,40?,41-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-(9Z,11Z)-Octadecadienoyl-2-isododecanoyl-sn-glycero-3-CDPHMDB
1-(9Z,11Z)-Octadecadienoyl-2-isododecanoyl-sn-glycero-3-cytidine-5'-diphosphateHMDB
CDP-DG(18:2/I-12:0)HMDB
CDP-DG(18:2N7/I-12:0)HMDB
CDP-DG(18:2W7/I-12:0)HMDB
CDP-DG(30:2)HMDB
CDP-Diacylglycerol(18:2(9Z,11Z)/I-12:0)HMDB
CDP-Diacylglycerol(18:2/I-12:0)HMDB
CDP-Diacylglycerol(18:2N7/I-12:0)HMDB
CDP-Diacylglycerol(18:2W7/I-12:0)HMDB
CDP-Diacylglycerol(30:2)HMDB
{[(2R,3R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-2-[(10-methylundecanoyl)oxy]-3-[(9Z,11Z)-octadeca-9,11-dienoyloxy]propoxy]phosphoryl}oxy)phosphinateHMDB
CDP-DG(18:2(9Z,11Z)/i-12:0)SMPDB
Chemical FormulaC42H73N3O15P2
Average Molecular Weight922.0
Monoisotopic Molecular Weight921.451692659
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-2-[(10-methylundecanoyl)oxy]-3-[(9Z,11Z)-octadeca-9,11-dienoyloxy]propoxy]phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-2-[(10-methylundecanoyl)oxy]-3-[(9Z,11Z)-octadeca-9,11-dienoyloxy]propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCC\C=C/C=C\CCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCC(C)C
InChI Identifier
InChI=1S/C42H73N3O15P2/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-20-23-26-37(46)55-30-34(58-38(47)27-24-21-18-17-19-22-25-33(2)3)31-56-61(51,52)60-62(53,54)57-32-35-39(48)40(49)41(59-35)45-29-28-36(43)44-42(45)50/h9-12,28-29,33-35,39-41,48-49H,4-8,13-27,30-32H2,1-3H3,(H,51,52)(H,53,54)(H2,43,44,50)/b10-9-,12-11-/t34-,35-,39+,40?,41-/m1/s1
InChI KeyAGPRHJMUWDCGEI-JEZDYYCXSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cdp-diacylglycerols. These are glycerolipids containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassCDP-glycerols
Direct ParentCDP-diacylglycerols
Alternative Parents
Substituents
  • Cdp-diacylglycerol
  • Pyrimidine ribonucleoside diphosphate
  • Diacyl-glycerol-3-pyrophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Fatty acid ester
  • Monoalkyl phosphate
  • Hydroxypyrimidine
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Alkyl phosphate
  • Hydropyrimidine
  • Pyrimidine
  • Phosphoric acid ester
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Carboxylic acid ester
  • 1,2-diol
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Carboxylic acid derivative
  • Organopnictogen compound
  • Organic oxide
  • Alcohol
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
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
logP5.47ALOGPS
logP7.79ChemAxon
logS-4.9ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.032ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area263.27 ŲChemAxon
Rotatable Bond Count37ChemAxon
Refractivity233.19 m³·mol⁻¹ChemAxon
Polarizability98.23 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
DeepCCS[M+H]+238.57130932474
DeepCCS[M-H]-236.74630932474
DeepCCS[M-2H]-270.33830932474
DeepCCS[M+Na]+244.26830932474
AllCCS[M+H]+292.832859911
AllCCS[M+H-H2O]+293.132859911
AllCCS[M+NH4]+292.532859911
AllCCS[M+Na]+292.432859911
AllCCS[M-H]-286.932859911
AllCCS[M+Na-2H]-293.732859911
AllCCS[M+HCOO]-301.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.9.44 minutes32390414
Predicted by Siyang on May 30, 202220.9291 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.81 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4007.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid146.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid292.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid184.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid645.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1182.5 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid1039.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)282.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2066.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1027.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1969.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid787.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid583.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate156.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA152.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water9.1 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-13Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 10V, Positive-QTOFsplash10-03di-0910000001-b9d64fbd73701d1822c72019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 20V, Positive-QTOFsplash10-03di-1910000000-ec60ca48a214906c97572019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 40V, Positive-QTOFsplash10-03di-3911000000-45341881b93bdab21fce2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 10V, Negative-QTOFsplash10-08or-0960001111-d3ba3d8db5d77ec64cbb2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 20V, Negative-QTOFsplash10-01t9-5982202001-703571a85d7655a8f1ab2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 40V, Negative-QTOFsplash10-0bvi-4910000000-870b879662910196bc0b2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 10V, Negative-QTOFsplash10-00di-0000000009-c71923ae9c431e282cdb2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 20V, Negative-QTOFsplash10-004l-9320800402-cf158258effb400a75fe2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 40V, Negative-QTOFsplash10-0kur-4609402102-b7dcdbf96c3cb3462ab02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 10V, Positive-QTOFsplash10-0fk9-4200010198-20913c815ce9ce4a1aeb2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 20V, Positive-QTOFsplash10-0a4j-7000000791-fb9f9ecad0ee0216f4622021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(18:2(9Z,11Z)/i-12:0) 40V, Positive-QTOFsplash10-000i-0149300000-41a0260bc53dffce3c892021-09-22Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID74877789
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131822708
PDB IDNot Available
ChEBI ID180871
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 ReferencesNot Available