Showing metabocard for CDP-DG(22:1(11Z)/24:1(9Z)) (MMDBc0056457)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-07-07 21:49:23 UTC
Update Date2023-12-14 16:53:41 UTC
Metabolite IDMMDBc0056457
Metabolite Identification
Common NameCDP-DG(22:1(11Z)/24:1(9Z))
DescriptionCDP-DG(22:1(11Z)/24:1(9Z)) is a cytidine diphosphate diacylglycerol or CDP-diacylglycerol. 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. CDP-DG(22:1(11Z)/24:1(9Z)), in particular, consists of one 11Z-docosenoyl chain at the C-1 position and one 9Z-tetracosenoyl chain at the C-2 position. In E. coli glycerophospholipid metabolism, the biosynthesis of CDP-diacylglycerol (CDP-DG) involves condensation of phosphatidic acid (PA) and cytidine triphosphate, with elimination of pyrophosphate, catalysed by the enzyme CDP-diacylglycerol synthase. The resulting CDP-diacylglycerol can be utilized immediately for the synthesis of phosphatidylglycerol (PG), and thence cardiolipin (CL), and of phosphatidylinositol (PI). CDP-DG(22:1(11Z)/24:1(9Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00005634bf7ddc88>

CDP-DG(22:1(11Z)/24:1(9Z))
  Mrv1652312131917132D          

 79 80  0  0  0  0            999 V2000
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M  END
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3D MOL for #<Metabolite:0x00005634bf7ddc88>

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3D SDF for #<Metabolite:0x00005634bf7ddc88>
CDP-DG(22:1(11Z)/24:1(9Z))
  Mrv1652312131917132D          

 79 80  0  0  0  0            999 V2000
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  -15.0464   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -16.4746   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.1887   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.9028   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -18.6170   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -19.3311   -0.3281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -20.0452   -0.7412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  3  5  1  1  0  0  0
  2  1  1  0  0  0  0
  3  6  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 17  1  0  0  0  0
 11 18  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 25 26  1  0  0  0  0
 26 21  1  0  0  0  0
 21 19  2  0  0  0  0
 23 20  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 27 28  1  0  0  0  0
 27 31  1  0  0  0  0
 29  7  1  6  0  0  0
 28 26  1  1  0  0  0
 31  9  1  1  0  0  0
 30  8  1  6  0  0  0
 14  4  1  0  0  0  0
  1 32  1  0  0  0  0
  6 55  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  2  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  1  0  0  0  0
 51 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 55 56  2  0  0  0  0
 55 57  1  0  0  0  0
 57 58  1  0  0  0  0
 58 59  1  0  0  0  0
 59 60  1  0  0  0  0
 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 64 65  2  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 67 68  1  0  0  0  0
 68 69  1  0  0  0  0
 69 70  1  0  0  0  0
 70 71  1  0  0  0  0
 71 72  1  0  0  0  0
 72 73  1  0  0  0  0
 73 74  1  0  0  0  0
 74 75  1  0  0  0  0
 75 76  1  0  0  0  0
 76 77  1  0  0  0  0
 77 78  1  0  0  0  0
 78 79  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056457

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C58H105N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-24-26-28-30-32-34-36-38-40-42-44-54(63)74-50(47-71-53(62)43-41-39-37-35-33-31-29-27-25-22-20-18-16-14-12-10-8-6-4-2)48-72-77(67,68)76-78(69,70)73-49-51-55(64)56(65)57(75-51)61-46-45-52(59)60-58(61)66/h22,25,28,30,45-46,50-51,55-57,64-65H,3-21,23-24,26-27,29,31-44,47-49H2,1-2H3,(H,67,68)(H,69,70)(H2,59,60,66)/b25-22-,30-28-/t50-,51-,55-,56-,57-/m1/s1

> <INCHI_KEY>
JJLRZCBPLJKYDF-LEOWYTOUSA-N

> <FORMULA>
C58H105N3O15P2

> <MOLECULAR_WEIGHT>
1146.432

> <EXACT_MASS>
1145.702093689

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
183

> <JCHEM_AVERAGE_POLARIZABILITY>
132.35478952525807

> <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}({[(2R)-3-[(11Z)-docos-11-enoyloxy]-2-[(9Z)-tetracos-9-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
8.43

> <JCHEM_LOGP>
15.05686777533333

> <ALOGPS_LOGS>
-6.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.27162555362587

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8631673662376511

> <JCHEM_PKA_STRONGEST_BASIC>
-0.03198989821723941

> <JCHEM_POLAR_SURFACE_AREA>
263.27000000000004

> <JCHEM_REFRACTIVITY>
306.8577

> <JCHEM_ROTATABLE_BOND_COUNT>
54

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.41e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-3-[(11Z)-docos-11-enoyloxy]-2-[(9Z)-tetracos-9-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for #<Metabolite:0x00005634bf7ddc88>
Download
PDB for #<Metabolite:0x00005634bf7ddc88>
HEADER    PROTEIN                                 13-DEC-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(22:1(11Z)/24:1(9Z))                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-DEC-19         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  -0.664   0.000  0.00  0.00           H+0
HETATM    6  O   UNK     0      -5.217  -0.664   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   1.463   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   1.463   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       0.890   0.694   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      -0.456   1.444   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -1.790   0.671   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.290   2.790   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.251   2.763   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.997   2.801   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.456   2.801   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      11.394  -0.846   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      14.067   3.776   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      11.394   0.692   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0      12.729   1.463   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      12.729   3.005   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.394   3.776   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.059   3.005   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      10.059   1.463   0.000  0.00  0.00           N+0
HETATM   27  O   UNK     0       7.473   1.619   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.720   0.712   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.244  -0.754   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.702  -0.754   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.225   0.712   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -8.423   1.436   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -8.423   2.876   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -9.756   0.665   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -11.089   1.436   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -12.422   0.665   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -13.755   1.436   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -15.088   0.665   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -16.421   1.436   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -17.754   0.665   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -19.087   1.436   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -20.420   0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -21.753   1.436   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -23.293   1.436   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -24.626   0.665   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -25.959   1.436   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -27.292   0.665   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -28.625   1.436   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -29.958   0.665   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -31.291   1.436   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -32.624   0.665   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -33.957   1.436   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -35.290   0.665   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -36.623   1.436   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -6.551  -1.384   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      -6.551  -2.824   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0      -7.884  -0.612   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -9.217  -1.384   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -10.550  -0.612   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -11.883  -1.384   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -13.216  -0.612   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -14.549  -1.384   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -15.882  -0.612   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -17.215  -1.384   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -18.755  -1.384   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -20.088  -0.612   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -21.421  -1.384   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0     -22.754  -0.612   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0     -24.087  -1.384   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0     -25.420  -0.612   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0     -26.754  -1.384   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0     -28.087  -0.612   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0     -29.420  -1.384   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0     -30.753  -0.612   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0     -32.086  -1.384   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0     -33.419  -0.612   0.000  0.00  0.00           C+0
HETATM   77  C   UNK     0     -34.752  -1.384   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0     -36.085  -0.612   0.000  0.00  0.00           C+0
HETATM   79  C   UNK     0     -37.418  -1.384   0.000  0.00  0.00           C+0
CONECT    1    2   32                                                       
CONECT    2    3    1                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3   14                                                       
CONECT    5    3                                                            
CONECT    6    3   55                                                       
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   26   19                                                  
CONECT   22   21   23                                                       
CONECT   23   24   22   20                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   21   28                                                  
CONECT   27   28   31                                                       
CONECT   28   29   27   26                                                  
CONECT   29   28   30    7                                                  
CONECT   30   29   31    8                                                  
CONECT   31   30   27    9                                                  
CONECT   32    1   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53                                                            
CONECT   55    6   56   57                                                  
CONECT   56   55                                                            
CONECT   57   55   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                                                       
CONECT   76   75   77                                                       
CONECT   77   76   78                                                       
CONECT   78   77   79                                                       
CONECT   79   78                                                            
MASTER        0    0    0    0    0    0    0    0   79    0  160    0
END

Download
3D PDB for #<Metabolite:0x00005634bf7ddc88>
Download
SMILES for #<Metabolite:0x00005634bf7ddc88>
[H][C@@](COC(=O)CCCCCCCCC\C=C/CCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCC\C=C/CCCCCCCCCCCCCC
Download
INCHI for #<Metabolite:0x00005634bf7ddc88>
InChI=1S/C58H105N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-24-26-28-30-32-34-36-38-40-42-44-54(63)74-50(47-71-53(62)43-41-39-37-35-33-31-29-27-25-22-20-18-16-14-12-10-8-6-4-2)48-72-77(67,68)76-78(69,70)73-49-51-55(64)56(65)57(75-51)61-46-45-52(59)60-58(61)66/h22,25,28,30,45-46,50-51,55-57,64-65H,3-21,23-24,26-27,29,31-44,47-49H2,1-2H3,(H,67,68)(H,69,70)(H2,59,60,66)/b25-22-,30-28-/t50-,51-,55-,56-,57-/m1/s1
Download
Synonyms
ValueSource
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({[(2R)-3-[(11Z)-docos-11-enoyloxy]-2-[(9Z)-tetracos-9-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)phosphinateGenerator
Molecular FormulaC58H105N3O15P2
Average Mass1146.432
Monoisotopic Mass1145.702093689
IUPAC Name{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-3-[(11Z)-docos-11-enoyloxy]-2-[(9Z)-tetracos-9-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-3-[(11Z)-docos-11-enoyloxy]-2-[(9Z)-tetracos-9-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCC\C=C/CCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCC\C=C/CCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C58H105N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-24-26-28-30-32-34-36-38-40-42-44-54(63)74-50(47-71-53(62)43-41-39-37-35-33-31-29-27-25-22-20-18-16-14-12-10-8-6-4-2)48-72-77(67,68)76-78(69,70)73-49-51-55(64)56(65)57(75-51)61-46-45-52(59)60-58(61)66/h22,25,28,30,45-46,50-51,55-57,64-65H,3-21,23-24,26-27,29,31-44,47-49H2,1-2H3,(H,67,68)(H,69,70)(H2,59,60,66)/b25-22-,30-28-/t50-,51-,55-,56-,57-/m1/s1
InChI KeyJJLRZCBPLJKYDF-LEOWYTOUSA-N