Showing metabocard for CDP-DG(18:0/25:1(9Z)) (MMDBc0044270)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 12:53:02 UTC
Update Date2022-09-01 00:14:50 UTC
Metabolite IDMMDBc0044270
Metabolite Identification
Common NameCDP-DG(18:0/25:1(9Z))
DescriptionCDP-DG(18:0/25:1(9Z)) belongs to the family of CDP-diacylglycerols. It is a glycerophospholipid containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part. As is the case with diacylglycerols, phosphatidylserines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. CDP-DG(18:0/25:1(9Z)), in particular, consists of two octadecanoyl chain at positions C-1 and C2. 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(18:0/25:1(9Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007fdb386a75c8>

CDP-DG(18:0/25:1(9Z))
  Mrv1652306201617122D          

 76 77  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
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   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
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   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
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3D MOL for #<Metabolite:0x00007fdb386a75c8>

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3D SDF for #<Metabolite:0x00007fdb386a75c8>
CDP-DG(18:0/25:1(9Z))
  Mrv1652306201617122D          

 76 77  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
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  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  8  4  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  2  0  0  0  0
 12 10  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  2  0  0  0  0
 14 23  1  0  0  0  0
 16 17  1  0  0  0  0
 16 22  1  1  0  0  0
 18 19  1  0  0  0  0
 18 17  1  0  0  0  0
 18 27  1  1  0  0  0
 19 20  1  0  0  0  0
 20 16  1  0  0  0  0
 20 23  1  1  0  0  0
 21 17  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 25 27  1  0  0  0  0
 25 31  2  0  0  0  0
 26 28  1  0  0  0  0
 26 30  1  0  0  0  0
 27 29  1  0  0  0  0
 28 29  2  0  0  0  0
 32  5  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  1  0  0  0  0
 44 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 51  6  1  0  0  0  0
 51 52  2  0  0  0  0
 51 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 58 59  1  0  0  0  0
 59 60  1  0  0  0  0
 60 61  2  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  1  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 67 68  1  0  0  0  0
 68 69  1  0  0  0  0
 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
M  END
> <DATABASE_ID>
MMDBc0044270

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C55H101N3O15P2/c1-3-5-7-9-11-13-15-17-19-20-21-22-23-24-25-27-29-31-33-35-37-39-41-51(60)71-47(44-68-50(59)40-38-36-34-32-30-28-26-18-16-14-12-10-8-6-4-2)45-69-74(64,65)73-75(66,67)70-46-48-52(61)53(62)54(72-48)58-43-42-49(56)57-55(58)63/h25,27,42-43,47-48,52-54,61-62H,3-24,26,28-41,44-46H2,1-2H3,(H,64,65)(H,66,67)(H2,56,57,63)/b27-25-/t47-,48-,52+,53?,54-/m1/s1

> <INCHI_KEY>
VMGYXNNNSBYVQV-UZOQDRLSSA-N

> <FORMULA>
C55H101N3O15P2

> <MOLECULAR_WEIGHT>
1106.367

> <EXACT_MASS>
1105.67079356

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
176

> <JCHEM_AVERAGE_POLARIZABILITY>
126.69332071696343

> <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-(octadecanoyloxy)-2-[(9Z)-pentacos-9-enoyloxy]propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
8.04

> <JCHEM_LOGP>
14.085083437000002

> <ALOGPS_LOGS>
-6.25

> <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>
291.9381

> <JCHEM_ROTATABLE_BOND_COUNT>
52

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.29e-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-(octadecanoyloxy)-2-[(9Z)-pentacos-9-enoyloxy]propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for #<Metabolite:0x00007fdb386a75c8>
Download
PDB for #<Metabolite:0x00007fdb386a75c8>
HEADER    PROTEIN                                 20-JUN-16   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(18:0/25:1(9Z))                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-16         0                                  
HETATM    1  C   UNK     0      32.564  -7.496   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      30.770  -8.532   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      28.976  -7.496   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      34.358  -8.532   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      27.181  -8.532   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      29.370 -10.604   0.000  0.00  0.00           O+0
HETATM    7  H   UNK     0      32.332 -10.683   0.000  0.00  0.00           H+0
HETATM    8  P   UNK     0      36.357  -7.853   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0      36.357  -9.962   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      38.832  -8.477   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      36.357  -5.947   0.000  0.00  0.00           O+0
HETATM   12  P   UNK     0      40.830  -7.798   0.000  0.00  0.00           P+0
HETATM   13  O   UNK     0      40.830  -9.907   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      43.305  -8.422   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      40.830  -5.892   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      46.963 -12.597   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      50.084 -12.597   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      51.776 -10.958   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      48.636  -9.722   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      44.997 -10.940   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      50.093 -14.090   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      46.952 -14.112   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      44.990  -9.400   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      53.036  -6.313   0.000  0.00  0.00           N+0
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      13.850  -8.533   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      12.517  -7.762   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      11.184  -8.533   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       9.851  -7.762   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       8.518  -8.533   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       7.185  -7.762   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       5.852  -8.533   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       4.519  -7.762   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       3.185  -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      15.831 -11.374   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      14.498 -10.603   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      13.165 -11.374   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      11.832 -10.603   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      10.499 -11.374   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0       9.166 -10.603   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0       7.833 -11.374   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0       6.500 -10.603   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0       5.167 -11.374   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0       3.834 -10.603   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0       2.501 -11.374   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0       1.168 -10.603   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0      -0.165 -11.374   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0      -1.498 -10.603   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0      -2.831 -11.374   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0      -4.164 -10.603   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                                                       
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                                                            
MASTER        0    0    0    0    0    0    0    0   76    0  154    0
END

Download
3D PDB for #<Metabolite:0x00007fdb386a75c8>
Download
SMILES for #<Metabolite:0x00007fdb386a75c8>
[H][C@@](COC(=O)CCCCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCC\C=C/CCCCCCCCCCCCCCC
Download
INCHI for #<Metabolite:0x00007fdb386a75c8>
InChI=1S/C55H101N3O15P2/c1-3-5-7-9-11-13-15-17-19-20-21-22-23-24-25-27-29-31-33-35-37-39-41-51(60)71-47(44-68-50(59)40-38-36-34-32-30-28-26-18-16-14-12-10-8-6-4-2)45-69-74(64,65)73-75(66,67)70-46-48-52(61)53(62)54(72-48)58-43-42-49(56)57-55(58)63/h25,27,42-43,47-48,52-54,61-62H,3-24,26,28-41,44-46H2,1-2H3,(H,64,65)(H,66,67)(H2,56,57,63)/b27-25-/t47-,48-,52+,53?,54-/m1/s1
Download
SynonymsNot Available
Molecular FormulaC55H101N3O15P2
Average Mass1106.367
Monoisotopic Mass1105.67079356
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-(octadecanoyloxy)-2-[(9Z)-pentacos-9-enoyloxy]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-(octadecanoyloxy)-2-[(9Z)-pentacos-9-enoyloxy]propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCC\C=C/CCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C55H101N3O15P2/c1-3-5-7-9-11-13-15-17-19-20-21-22-23-24-25-27-29-31-33-35-37-39-41-51(60)71-47(44-68-50(59)40-38-36-34-32-30-28-26-18-16-14-12-10-8-6-4-2)45-69-74(64,65)73-75(66,67)70-46-48-52(61)53(62)54(72-48)58-43-42-49(56)57-55(58)63/h25,27,42-43,47-48,52-54,61-62H,3-24,26,28-41,44-46H2,1-2H3,(H,64,65)(H,66,67)(H2,56,57,63)/b27-25-/t47-,48-,52+,53?,54-/m1/s1
InChI KeyVMGYXNNNSBYVQV-UZOQDRLSSA-N