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Showing metabocard for CDP-DG(i-20:0/i-24:0) (HMDB0116311)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 07:49:18 UTC
Update Date2022-11-30 19:26:33 UTC
HMDB IDHMDB0116311
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(i-20:0/i-24:0)
DescriptionCDP-DG(i-20:0/i-24:0) 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(i-20:0/i-24:0), in particular, consists of one chain of isoeicosanoic acid at the C-1 position and one chain of isotetracosanoic 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?1563873700
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116311 (CDP-DG(i-20:0/i-24:0))

CDP-DG(i-20:0/i-24:0)
  Mrv1652309161722392D          

 77 78  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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   25.1589   -6.7486    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0116311 (CDP-DG(i-20:0/i-24:0))

HMDB0116311
     RDKit          3D
CDP-DG(i-20:0/i-24:0)
181182  0  0  0  0  0  0  0  0999 V2000
    6.4498   -4.0480   -1.9195 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9040   -5.3615   -1.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8785   -5.8900   -2.3866 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2922   -5.1046   -0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7264   -6.3403    0.5232 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2300   -6.3076    1.8972 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1995   -5.3603    2.3582 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6382   -3.9516    2.4072 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5258   -3.0248    2.9006 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3098   -3.0570    2.0131 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6097   -2.6489    0.6083 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116311 (CDP-DG(i-20:0/i-24:0))

CDP-DG(i-20:0/i-24:0)
  Mrv1652309161722392D          

 77 78  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0116311

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C56H105N3O15P2/c1-46(2)37-33-29-25-21-17-13-9-7-5-6-8-10-16-20-24-28-32-36-40-52(61)72-48(43-69-51(60)39-35-31-27-23-19-15-12-11-14-18-22-26-30-34-38-47(3)4)44-70-75(65,66)74-76(67,68)71-45-49-53(62)54(63)55(73-49)59-42-41-50(57)58-56(59)64/h41-42,46-49,53-55,62-63H,5-40,43-45H2,1-4H3,(H,65,66)(H,67,68)(H2,57,58,64)/t48-,49-,53+,54?,55-/m1/s1

> <INCHI_KEY>
XKBUFMBNBHWDQJ-CKZKIYGOSA-N

> <FORMULA>
C56H105N3O15P2

> <MOLECULAR_WEIGHT>
1122.41

> <EXACT_MASS>
1121.702093689

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
181

> <JCHEM_AVERAGE_POLARIZABILITY>
129.7212349528972

> <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)-3-[(18-methylnonadecanoyl)oxy]-2-[(22-methyltricosanoyl)oxy]propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
7.77

> <JCHEM_LOGP>
14.576474621333332

> <ALOGPS_LOGS>
-6.36

> <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>
295.3177

> <JCHEM_ROTATABLE_BOND_COUNT>
52

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.94e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-[(18-methylnonadecanoyl)oxy]-2-[(22-methyltricosanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116311 (CDP-DG(i-20:0/i-24:0))

HMDB0116311
     RDKit          3D
CDP-DG(i-20:0/i-24:0)
181182  0  0  0  0  0  0  0  0999 V2000
    6.4498   -4.0480   -1.9195 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9040   -5.3615   -1.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8785   -5.8900   -2.3866 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2922   -5.1046   -0.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7264   -6.3403    0.5232 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2300   -6.3076    1.8972 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1995   -5.3603    2.3582 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6382   -3.9516    2.4072 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5258   -3.0248    2.9006 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3098   -3.0570    2.0131 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6097   -2.6489    0.6083 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.2612    2.3151   -7.1112 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1965    3.3485   -5.9768 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2772    0.9358   -5.0822 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6742   -0.0841   -5.9644 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3811   -1.4430   -5.3792 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0195   -1.5109   -5.1678 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4366   -2.2668   -6.1515 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6132   -1.5609   -6.8026 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8814   -0.2948   -6.4290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8664    0.4642   -6.9913 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4810   -2.8255   -7.0605 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3644   -4.2062   -7.2159 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.8495   -2.2847   -7.0963 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0116311 (CDP-DG(i-20:0/i-24:0))

HEADER    PROTEIN                                 16-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(i-20:0/i-24:0)                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-SEP-17         0                                  
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HETATM   73  C   UNK     0       2.708 -10.603   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0       1.375 -11.374   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0       0.042 -10.603   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0      -1.291 -11.374   0.000  0.00  0.00           C+0
HETATM   77  C   UNK     0      -1.291  -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   53                                                       
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   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50                                                            
CONECT   53    6   54   55                                                  
CONECT   54   53                                                            
CONECT   55   53   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69                                                       
CONECT   69   68   70                                                       
CONECT   70   69   71                                                       
CONECT   71   70   72                                                       
CONECT   72   71   73                                                       
CONECT   73   72   74                                                       
CONECT   74   73   75                                                       
CONECT   75   74   76   77                                                  
CONECT   76   75                                                            
CONECT   77   75                                                            
MASTER        0    0    0    0    0    0    0    0   77    0  156    0
END
Download

3D PDB for HMDB0116311 (CDP-DG(i-20:0/i-24:0))

COMPND    HMDB0116311
HETATM    1  C1  UNL     1       6.450  -4.048  -1.920  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.904  -5.361  -1.437  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.878  -5.890  -2.387  1.00  0.00           C  
HETATM    4  C4  UNL     1       5.292  -5.105  -0.038  1.00  0.00           C  
HETATM    5  C5  UNL     1       4.726  -6.340   0.523  1.00  0.00           C  
HETATM    6  C6  UNL     1       4.230  -6.308   1.897  1.00  0.00           C  
HETATM    7  C7  UNL     1       3.200  -5.360   2.358  1.00  0.00           C  
HETATM    8  C8  UNL     1       3.638  -3.952   2.407  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.526  -3.025   2.901  1.00  0.00           C  
HETATM   10  C10 UNL     1       1.310  -3.057   2.013  1.00  0.00           C  
HETATM   11  C11 UNL     1       1.610  -2.649   0.608  1.00  0.00           C  
HETATM   12  C12 UNL     1       0.380  -2.661  -0.263  1.00  0.00           C  
HETATM   13  C13 UNL     1      -0.672  -1.713   0.215  1.00  0.00           C  
HETATM   14  C14 UNL     1      -1.911  -1.667  -0.639  1.00  0.00           C  
HETATM   15  C15 UNL     1      -1.536  -1.265  -2.025  1.00  0.00           C  
HETATM   16  C16 UNL     1      -2.719  -1.136  -2.964  1.00  0.00           C  
HETATM   17  C17 UNL     1      -3.695  -0.085  -2.452  1.00  0.00           C  
HETATM   18  C18 UNL     1      -2.988   1.261  -2.329  1.00  0.00           C  
HETATM   19  C19 UNL     1      -3.976   2.278  -1.815  1.00  0.00           C  
HETATM   20  C20 UNL     1      -3.389   3.659  -1.655  1.00  0.00           C  
HETATM   21  C21 UNL     1      -2.224   3.573  -0.666  1.00  0.00           C  
HETATM   22  C22 UNL     1      -1.601   4.920  -0.445  1.00  0.00           C  
HETATM   23  C23 UNL     1      -0.493   4.870   0.550  1.00  0.00           C  
HETATM   24  C24 UNL     1       0.607   3.970   0.183  1.00  0.00           C  
HETATM   25  O1  UNL     1       0.503   2.806  -0.254  1.00  0.00           O  
HETATM   26  O2  UNL     1       1.937   4.444   0.323  1.00  0.00           O  
HETATM   27  C25 UNL     1       3.017   3.609  -0.038  1.00  0.00           C  
HETATM   28  C26 UNL     1       4.142   3.675   0.901  1.00  0.00           C  
HETATM   29  O3  UNL     1       3.979   3.315   2.205  1.00  0.00           O  
HETATM   30  C27 UNL     1       3.601   2.180   2.822  1.00  0.00           C  
HETATM   31  O4  UNL     1       3.273   1.198   2.073  1.00  0.00           O  
HETATM   32  C28 UNL     1       3.562   2.013   4.287  1.00  0.00           C  
HETATM   33  C29 UNL     1       3.226   0.658   4.775  1.00  0.00           C  
HETATM   34  C30 UNL     1       1.813   0.170   4.524  1.00  0.00           C  
HETATM   35  C31 UNL     1       0.875   1.051   5.255  1.00  0.00           C  
HETATM   36  C32 UNL     1      -0.591   0.645   5.186  1.00  0.00           C  
HETATM   37  C33 UNL     1      -0.760  -0.698   5.745  1.00  0.00           C  
HETATM   38  C34 UNL     1      -2.028  -1.348   5.995  1.00  0.00           C  
HETATM   39  C35 UNL     1      -3.126  -1.645   5.112  1.00  0.00           C  
HETATM   40  C36 UNL     1      -4.054  -0.668   4.575  1.00  0.00           C  
HETATM   41  C37 UNL     1      -3.654   0.462   3.730  1.00  0.00           C  
HETATM   42  C38 UNL     1      -4.978   1.186   3.337  1.00  0.00           C  
HETATM   43  C39 UNL     1      -4.645   2.352   2.437  1.00  0.00           C  
HETATM   44  C40 UNL     1      -3.718   3.344   3.054  1.00  0.00           C  
HETATM   45  C41 UNL     1      -4.224   3.995   4.303  1.00  0.00           C  
HETATM   46  C42 UNL     1      -5.485   4.781   4.134  1.00  0.00           C  
HETATM   47  C43 UNL     1      -5.329   5.910   3.137  1.00  0.00           C  
HETATM   48  C44 UNL     1      -6.637   6.644   3.050  1.00  0.00           C  
HETATM   49  C45 UNL     1      -7.778   5.790   2.602  1.00  0.00           C  
HETATM   50  C46 UNL     1      -6.540   7.842   2.120  1.00  0.00           C  
HETATM   51  C47 UNL     1       3.513   4.119  -1.443  1.00  0.00           C  
HETATM   52  O5  UNL     1       2.439   3.999  -2.296  1.00  0.00           O  
HETATM   53  P1  UNL     1       2.818   4.522  -3.846  1.00  0.00           P  
HETATM   54  O6  UNL     1       1.574   4.962  -4.587  1.00  0.00           O  
HETATM   55  O7  UNL     1       3.844   5.875  -3.794  1.00  0.00           O  
HETATM   56  O8  UNL     1       3.615   3.316  -4.694  1.00  0.00           O  
HETATM   57  P2  UNL     1       2.601   2.459  -5.738  1.00  0.00           P  
HETATM   58  O9  UNL     1       3.261   2.315  -7.111  1.00  0.00           O  
HETATM   59  O10 UNL     1       1.197   3.348  -5.977  1.00  0.00           O  
HETATM   60  O11 UNL     1       2.277   0.936  -5.082  1.00  0.00           O  
HETATM   61  C48 UNL     1       2.674  -0.084  -5.964  1.00  0.00           C  
HETATM   62  C49 UNL     1       2.381  -1.443  -5.379  1.00  0.00           C  
HETATM   63  O12 UNL     1       1.019  -1.511  -5.168  1.00  0.00           O  
HETATM   64  C50 UNL     1       0.437  -2.267  -6.151  1.00  0.00           C  
HETATM   65  N1  UNL     1      -0.613  -1.561  -6.803  1.00  0.00           N  
HETATM   66  C51 UNL     1      -0.881  -0.295  -6.429  1.00  0.00           C  
HETATM   67  C52 UNL     1      -1.866   0.464  -6.991  1.00  0.00           C  
HETATM   68  C53 UNL     1      -2.650  -0.087  -8.013  1.00  0.00           C  
HETATM   69  N2  UNL     1      -3.679   0.655  -8.629  1.00  0.00           N  
HETATM   70  N3  UNL     1      -2.365  -1.348  -8.368  1.00  0.00           N  
HETATM   71  C54 UNL     1      -1.383  -2.055  -7.783  1.00  0.00           C  
HETATM   72  O13 UNL     1      -1.201  -3.231  -8.194  1.00  0.00           O  
HETATM   73  C55 UNL     1       1.481  -2.826  -7.060  1.00  0.00           C  
HETATM   74  O14 UNL     1       1.364  -4.206  -7.216  1.00  0.00           O  
HETATM   75  C56 UNL     1       2.760  -2.566  -6.295  1.00  0.00           C  
HETATM   76  O15 UNL     1       3.850  -2.285  -7.096  1.00  0.00           O  
HETATM   77  H1  UNL     1       5.743  -3.255  -1.559  1.00  0.00           H  
HETATM   78  H2  UNL     1       6.519  -3.998  -3.026  1.00  0.00           H  
HETATM   79  H3  UNL     1       7.409  -3.861  -1.417  1.00  0.00           H  
HETATM   80  H4  UNL     1       6.705  -6.099  -1.343  1.00  0.00           H  
HETATM   81  H5  UNL     1       5.289  -5.787  -3.407  1.00  0.00           H  
HETATM   82  H6  UNL     1       4.762  -6.977  -2.195  1.00  0.00           H  
HETATM   83  H7  UNL     1       3.922  -5.346  -2.368  1.00  0.00           H  
HETATM   84  H8  UNL     1       6.024  -4.619   0.576  1.00  0.00           H  
HETATM   85  H9  UNL     1       4.400  -4.426  -0.282  1.00  0.00           H  
HETATM   86  H10 UNL     1       5.547  -7.135   0.417  1.00  0.00           H  
HETATM   87  H11 UNL     1       3.932  -6.788  -0.175  1.00  0.00           H  
HETATM   88  H12 UNL     1       3.893  -7.371   2.201  1.00  0.00           H  
HETATM   89  H13 UNL     1       5.120  -6.190   2.626  1.00  0.00           H  
HETATM   90  H14 UNL     1       2.917  -5.657   3.412  1.00  0.00           H  
HETATM   91  H15 UNL     1       2.266  -5.494   1.733  1.00  0.00           H  
HETATM   92  H16 UNL     1       4.405  -3.902   3.263  1.00  0.00           H  
HETATM   93  H17 UNL     1       4.122  -3.500   1.559  1.00  0.00           H  
HETATM   94  H18 UNL     1       2.211  -3.452   3.886  1.00  0.00           H  
HETATM   95  H19 UNL     1       2.925  -2.012   2.978  1.00  0.00           H  
HETATM   96  H20 UNL     1       0.602  -2.308   2.451  1.00  0.00           H  
HETATM   97  H21 UNL     1       0.806  -4.037   2.061  1.00  0.00           H  
HETATM   98  H22 UNL     1       2.042  -1.618   0.611  1.00  0.00           H  
HETATM   99  H23 UNL     1       2.367  -3.297   0.126  1.00  0.00           H  
HETATM  100  H24 UNL     1       0.000  -3.701  -0.347  1.00  0.00           H  
HETATM  101  H25 UNL     1       0.727  -2.406  -1.308  1.00  0.00           H  
HETATM  102  H26 UNL     1      -0.968  -1.975   1.262  1.00  0.00           H  
HETATM  103  H27 UNL     1      -0.204  -0.690   0.261  1.00  0.00           H  
HETATM  104  H28 UNL     1      -2.609  -0.960  -0.147  1.00  0.00           H  
HETATM  105  H29 UNL     1      -2.342  -2.699  -0.639  1.00  0.00           H  
HETATM  106  H30 UNL     1      -0.970  -0.338  -2.037  1.00  0.00           H  
HETATM  107  H31 UNL     1      -0.887  -2.048  -2.476  1.00  0.00           H  
HETATM  108  H32 UNL     1      -3.249  -2.084  -3.022  1.00  0.00           H  
HETATM  109  H33 UNL     1      -2.340  -0.788  -3.939  1.00  0.00           H  
HETATM  110  H34 UNL     1      -4.190  -0.382  -1.519  1.00  0.00           H  
HETATM  111  H35 UNL     1      -4.471   0.034  -3.232  1.00  0.00           H  
HETATM  112  H36 UNL     1      -2.649   1.545  -3.328  1.00  0.00           H  
HETATM  113  H37 UNL     1      -2.180   1.198  -1.561  1.00  0.00           H  
HETATM  114  H38 UNL     1      -4.841   2.371  -2.532  1.00  0.00           H  
HETATM  115  H39 UNL     1      -4.417   1.930  -0.858  1.00  0.00           H  
HETATM  116  H40 UNL     1      -3.005   4.030  -2.629  1.00  0.00           H  
HETATM  117  H41 UNL     1      -4.173   4.348  -1.290  1.00  0.00           H  
HETATM  118  H42 UNL     1      -1.448   2.961  -1.200  1.00  0.00           H  
HETATM  119  H43 UNL     1      -2.547   3.092   0.259  1.00  0.00           H  
HETATM  120  H44 UNL     1      -1.277   5.378  -1.413  1.00  0.00           H  
HETATM  121  H45 UNL     1      -2.393   5.600  -0.051  1.00  0.00           H  
HETATM  122  H46 UNL     1      -0.128   5.904   0.778  1.00  0.00           H  
HETATM  123  H47 UNL     1      -0.861   4.506   1.558  1.00  0.00           H  
HETATM  124  H48 UNL     1       2.730   2.574  -0.285  1.00  0.00           H  
HETATM  125  H49 UNL     1       4.561   4.745   0.913  1.00  0.00           H  
HETATM  126  H50 UNL     1       5.021   3.082   0.442  1.00  0.00           H  
HETATM  127  H51 UNL     1       2.823   2.770   4.684  1.00  0.00           H  
HETATM  128  H52 UNL     1       4.571   2.348   4.666  1.00  0.00           H  
HETATM  129  H53 UNL     1       3.939  -0.064   4.283  1.00  0.00           H  
HETATM  130  H54 UNL     1       3.420   0.535   5.870  1.00  0.00           H  
HETATM  131  H55 UNL     1       1.771  -0.881   4.923  1.00  0.00           H  
HETATM  132  H56 UNL     1       1.628   0.137   3.429  1.00  0.00           H  
HETATM  133  H57 UNL     1       0.926   2.077   4.807  1.00  0.00           H  
HETATM  134  H58 UNL     1       1.143   1.069   6.331  1.00  0.00           H  
HETATM  135  H59 UNL     1      -0.885   0.645   4.102  1.00  0.00           H  
HETATM  136  H60 UNL     1      -1.220   1.399   5.691  1.00  0.00           H  
HETATM  137  H61 UNL     1      -0.156  -0.766   6.733  1.00  0.00           H  
HETATM  138  H62 UNL     1      -0.110  -1.409   5.083  1.00  0.00           H  
HETATM  139  H63 UNL     1      -2.502  -0.810   6.933  1.00  0.00           H  
HETATM  140  H64 UNL     1      -1.800  -2.364   6.564  1.00  0.00           H  
HETATM  141  H65 UNL     1      -3.806  -2.467   5.610  1.00  0.00           H  
HETATM  142  H66 UNL     1      -2.707  -2.279   4.226  1.00  0.00           H  
HETATM  143  H67 UNL     1      -4.675  -0.192   5.431  1.00  0.00           H  
HETATM  144  H68 UNL     1      -4.925  -1.205   4.009  1.00  0.00           H  
HETATM  145  H69 UNL     1      -3.090   1.225   4.326  1.00  0.00           H  
HETATM  146  H70 UNL     1      -3.113   0.222   2.814  1.00  0.00           H  
HETATM  147  H71 UNL     1      -5.564   0.448   2.769  1.00  0.00           H  
HETATM  148  H72 UNL     1      -5.508   1.457   4.248  1.00  0.00           H  
HETATM  149  H73 UNL     1      -4.219   1.999   1.493  1.00  0.00           H  
HETATM  150  H74 UNL     1      -5.613   2.857   2.205  1.00  0.00           H  
HETATM  151  H75 UNL     1      -2.719   2.886   3.232  1.00  0.00           H  
HETATM  152  H76 UNL     1      -3.555   4.147   2.292  1.00  0.00           H  
HETATM  153  H77 UNL     1      -3.415   4.620   4.727  1.00  0.00           H  
HETATM  154  H78 UNL     1      -4.474   3.176   5.044  1.00  0.00           H  
HETATM  155  H79 UNL     1      -6.293   4.117   3.801  1.00  0.00           H  
HETATM  156  H80 UNL     1      -5.715   5.249   5.115  1.00  0.00           H  
HETATM  157  H81 UNL     1      -4.521   6.583   3.469  1.00  0.00           H  
HETATM  158  H82 UNL     1      -5.015   5.525   2.133  1.00  0.00           H  
HETATM  159  H83 UNL     1      -6.878   7.071   4.055  1.00  0.00           H  
HETATM  160  H84 UNL     1      -8.585   6.491   2.243  1.00  0.00           H  
HETATM  161  H85 UNL     1      -7.479   5.226   1.677  1.00  0.00           H  
HETATM  162  H86 UNL     1      -8.163   5.127   3.382  1.00  0.00           H  
HETATM  163  H87 UNL     1      -7.344   8.555   2.417  1.00  0.00           H  
HETATM  164  H88 UNL     1      -6.745   7.529   1.086  1.00  0.00           H  
HETATM  165  H89 UNL     1      -5.560   8.357   2.228  1.00  0.00           H  
HETATM  166  H90 UNL     1       3.938   5.115  -1.332  1.00  0.00           H  
HETATM  167  H91 UNL     1       4.298   3.408  -1.734  1.00  0.00           H  
HETATM  168  H92 UNL     1       4.631   5.695  -3.219  1.00  0.00           H  
HETATM  169  H93 UNL     1       0.454   2.879  -5.507  1.00  0.00           H  
HETATM  170  H94 UNL     1       3.704   0.036  -6.322  1.00  0.00           H  
HETATM  171  H95 UNL     1       2.028   0.078  -6.879  1.00  0.00           H  
HETATM  172  H96 UNL     1       2.881  -1.492  -4.393  1.00  0.00           H  
HETATM  173  H97 UNL     1      -0.036  -3.148  -5.623  1.00  0.00           H  
HETATM  174  H98 UNL     1      -0.302   0.179  -5.639  1.00  0.00           H  
HETATM  175  H99 UNL     1      -2.105   1.480  -6.714  1.00  0.00           H  
HETATM  176  HA0 UNL     1      -4.626   0.245  -8.710  1.00  0.00           H  
HETATM  177  HA1 UNL     1      -3.515   1.605  -9.005  1.00  0.00           H  
HETATM  178  HA2 UNL     1       1.487  -2.388  -8.064  1.00  0.00           H  
HETATM  179  HA3 UNL     1       0.973  -4.622  -6.391  1.00  0.00           H  
HETATM  180  HA4 UNL     1       3.051  -3.428  -5.656  1.00  0.00           H  
HETATM  181  HA5 UNL     1       3.674  -2.324  -8.061  1.00  0.00           H  
CONECT    1    2   77   78   79
CONECT    2    3    4   80
CONECT    3   81   82   83
CONECT    4    5   84   85
CONECT    5    6   86   87
CONECT    6    7   88   89
CONECT    7    8   90   91
CONECT    8    9   92   93
CONECT    9   10   94   95
CONECT   10   11   96   97
CONECT   11   12   98   99
CONECT   12   13  100  101
CONECT   13   14  102  103
CONECT   14   15  104  105
CONECT   15   16  106  107
CONECT   16   17  108  109
CONECT   17   18  110  111
CONECT   18   19  112  113
CONECT   19   20  114  115
CONECT   20   21  116  117
CONECT   21   22  118  119
CONECT   22   23  120  121
CONECT   23   24  122  123
CONECT   24   25   25   26
CONECT   26   27
CONECT   27   28   51  124
CONECT   28   29  125  126
CONECT   29   30
CONECT   30   31   31   32
CONECT   32   33  127  128
CONECT   33   34  129  130
CONECT   34   35  131  132
CONECT   35   36  133  134
CONECT   36   37  135  136
CONECT   37   38  137  138
CONECT   38   39  139  140
CONECT   39   40  141  142
CONECT   40   41  143  144
CONECT   41   42  145  146
CONECT   42   43  147  148
CONECT   43   44  149  150
CONECT   44   45  151  152
CONECT   45   46  153  154
CONECT   46   47  155  156
CONECT   47   48  157  158
CONECT   48   49   50  159
CONECT   49  160  161  162
CONECT   50  163  164  165
CONECT   51   52  166  167
CONECT   52   53
CONECT   53   54   54   55   56
CONECT   55  168
CONECT   56   57
CONECT   57   58   58   59   60
CONECT   59  169
CONECT   60   61
CONECT   61   62  170  171
CONECT   62   63   75  172
CONECT   63   64
CONECT   64   65   73  173
CONECT   65   66   71
CONECT   66   67   67  174
CONECT   67   68  175
CONECT   68   69   70   70
CONECT   69  176  177
CONECT   70   71
CONECT   71   72   72
CONECT   73   74   75  178
CONECT   74  179
CONECT   75   76  180
CONECT   76  181
END
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SMILES for HMDB0116311 (CDP-DG(i-20:0/i-24:0))

[H][C@@](COC(=O)CCCCCCCCCCCCCCCCC(C)C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCCCCCCCC(C)C
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INCHI for HMDB0116311 (CDP-DG(i-20:0/i-24:0))

InChI=1S/C56H105N3O15P2/c1-46(2)37-33-29-25-21-17-13-9-7-5-6-8-10-16-20-24-28-32-36-40-52(61)72-48(43-69-51(60)39-35-31-27-23-19-15-12-11-14-18-22-26-30-34-38-47(3)4)44-70-75(65,66)74-76(67,68)71-45-49-53(62)54(63)55(73-49)59-42-41-50(57)58-56(59)64/h41-42,46-49,53-55,62-63H,5-40,43-45H2,1-4H3,(H,65,66)(H,67,68)(H2,57,58,64)/t48-,49-,53+,54?,55-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-isoeicosanoyl-2-isotetracosanoyl-sn-glycero-3-CDPSMPDB, HMDB
1-isoeicosanoyl-2-isotetracosanoyl-sn-glycero-3-cytidine-5'-diphosphateSMPDB, HMDB
CDP-DG(i-20:0/i-24:0)SMPDB
CDP-DG(44:0)SMPDB, HMDB
CDP-diacylglycerol(i-20:0/i-24:0)SMPDB, HMDB
CDP-diacylglycerol(44:0)SMPDB, HMDB
{[(2R,3R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(18-methylnonadecanoyl)oxy]-2-[(22-methyltricosanoyl)oxy]propoxy]phosphoryl}oxy)phosphinateGenerator, HMDB
Chemical FormulaC56H105N3O15P2
Average Molecular Weight1122.41
Monoisotopic Molecular Weight1121.702093689
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(18-methylnonadecanoyl)oxy]-2-[(22-methyltricosanoyl)oxy]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)-3-[(18-methylnonadecanoyl)oxy]-2-[(22-methyltricosanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCCCCCC(C)C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCCCCCCCC(C)C
InChI Identifier
InChI=1S/C56H105N3O15P2/c1-46(2)37-33-29-25-21-17-13-9-7-5-6-8-10-16-20-24-28-32-36-40-52(61)72-48(43-69-51(60)39-35-31-27-23-19-15-12-11-14-18-22-26-30-34-38-47(3)4)44-70-75(65,66)74-76(67,68)71-45-49-53(62)54(63)55(73-49)59-42-41-50(57)58-56(59)64/h41-42,46-49,53-55,62-63H,5-40,43-45H2,1-4H3,(H,65,66)(H,67,68)(H2,57,58,64)/t48-,49-,53+,54?,55-/m1/s1
InChI KeyXKBUFMBNBHWDQJ-CKZKIYGOSA-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
DispositionNot Available
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
logP7.77ALOGPS
logP14.58ChemAxon
logS-6.4ALOGPS
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 Count52ChemAxon
Refractivity295.32 m³·mol⁻¹ChemAxon
Polarizability129.72 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]+297.62330932474
DeepCCS[M-H]-295.9630932474
DeepCCS[M-2H]-329.99430932474
DeepCCS[M+Na]+303.7730932474
AllCCS[M+H]+336.432859911
AllCCS[M+H-H2O]+336.732859911
AllCCS[M+NH4]+336.232859911
AllCCS[M+Na]+336.132859911
AllCCS[M-H]-305.232859911
AllCCS[M+Na-2H]-310.732859911
AllCCS[M+HCOO]-316.732859911

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - CDP-DG(i-20:0/i-24:0) 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(i-20:0/i-24:0) 10V, Positive-QTOFsplash10-03di-0911000100-54b9130c4ebf54540f052019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 20V, Positive-QTOFsplash10-03di-1911000110-baa7e897c55011a4c2312019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 40V, Positive-QTOFsplash10-03di-3912000000-388f948aa749f919cc0c2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 10V, Negative-QTOFsplash10-08fu-1936000110-f0e10ebfc08f3e26bb3f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 20V, Negative-QTOFsplash10-03di-5839110020-05ad208ae5de01ebcd542019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 40V, Negative-QTOFsplash10-0bvi-5903000000-bcec4a85549e1815fcdc2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 10V, Negative-QTOFsplash10-00di-0901000100-4476a4fda7ce27f43ee72021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 20V, Negative-QTOFsplash10-004l-9114400200-26a34a728e8039dfdc1a2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 40V, Negative-QTOFsplash10-0kea-6419130200-4b9a261bd0a706f492362021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 10V, Positive-QTOFsplash10-00di-9801000201-e754bb2e9d860911faff2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 20V, Positive-QTOFsplash10-0q29-9200000005-2d966e7ad075a344dfa12021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-20:0/i-24:0) 40V, Positive-QTOFsplash10-0ab9-0015970000-1fbbd290007b857070962021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131822967
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 ReferencesNot Available