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Showing metabocard for CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) (HMDB0006973)

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enzymes (4) Show 4 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-09-12 01:12:23 UTC
Update Date2022-11-30 19:02:48 UTC
HMDB IDHMDB0006973
Secondary Accession Numbers
  • HMDB06973
Metabolite Identification
Common NameCDP-DG(16:0/20:4(5Z,8Z,11Z,14Z))
DescriptionCDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) is a cytidine diphosphate diacylglycerol or CDP-diacylglycerol. CDP-diacylglycerol (CDP-DG) 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(16:0/20:4(5Z,8Z,11Z,14Z)), in particular, consists of one chain of palmitic acid at the C-1 position and one chain of arachidonic acid at the C-2 position. The palmitic acid moiety is derived from fish oils, milk fats, vegetable oils and animal fats, while the arachidonic acid moiety is derived from animal fats and eggs. CDP-diacylglycerols are intermediates in the synthesis of phosphatidylglycerols (PG, PC, PS, PI), which is catalyzed by CDP-diacyl synthase, synthase, phosphatidylglycerolphosphate (PGP) synthase, phosphatidylinositol (PI) synthase, and phosphatidylserine (PS) synthase. 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?1582752416
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0006973 (CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)))


  Mrv0541 02231220572D          

 69 70  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0006973 (CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)))

HMDB0006973
     RDKit          3D
CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z))
149150  0  0  0  0  0  0  0  0999 V2000
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   -1.5285   -7.7849   -6.3447 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0006973 (CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)))


  Mrv0541 02231220572D          

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 63 64  2  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  6  1  0  0  0  0
 68 69  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006973

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C48H81N3O15P2/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-44(53)64-40(37-61-43(52)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2)38-62-67(57,58)66-68(59,60)63-39-41-45(54)46(55)47(65-41)51-36-35-42(49)50-48(51)56/h11,13,17-18,20,22,26,28,35-36,40-41,45-47,54-55H,3-10,12,14-16,19,21,23-25,27,29-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b13-11-,18-17-,22-20-,28-26-/t40-,41-,45+,46?,47-/m1/s1

> <INCHI_KEY>
GMBXECXXNMMIAN-HUOFUYQBSA-N

> <FORMULA>
C48H81N3O15P2

> <MOLECULAR_WEIGHT>
1002.1154

> <EXACT_MASS>
1001.514291961

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
108.52242322941416

> <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)phosphoryl)oxy][(2R)-3-(hexadecanoyloxy)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy]phosphinic acid

> <ALOGPS_LOGP>
6.86

> <JCHEM_LOGP>
9.612966956637633

> <ALOGPS_LOGS>
-5.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2529758511196185

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.859045346136682

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5215044803626353

> <JCHEM_POLAR_SURFACE_AREA>
263.27

> <JCHEM_REFRACTIVITY>
263.08090000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
42

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.63e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(2R)-3-(hexadecanoyloxy)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxyphosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0006973 (CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)))

HMDB0006973
     RDKit          3D
CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z))
149150  0  0  0  0  0  0  0  0999 V2000
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   -2.6208   -5.6843   -5.7295 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8160   -4.8272   -5.7880 C   0  0  0  0  0  0  0  0  0  0  0  0
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 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  1  0
 37 38  1  0
 38 39  1  0
 39 40  1  0
 40 41  1  0
 41 42  1  0
 23 43  1  0
 43 44  1  0
 44 45  1  0
 45 46  2  0
 45 47  1  0
 45 48  1  0
 48 49  1  0
 49 50  2  0
 49 51  1  0
 49 52  1  0
 52 53  1  0
 53 54  1  0
 54 55  1  0
 55 56  1  0
 56 57  1  0
 57 58  1  0
 58 59  2  0
 59 60  1  0
 60 61  1  0
 60 62  2  0
 62 63  1  0
 63 64  2  0
 56 65  1  0
 65 66  1  0
 65 67  1  0
 67 68  1  0
 67 54  1  0
 63 57  1  0
  1 69  1  0
  1 70  1  0
  1 71  1  0
  2 72  1  0
  2 73  1  0
  3 74  1  0
  3 75  1  0
  4 76  1  0
  4 77  1  0
  5 78  1  0
  5 79  1  0
  6 80  1  0
  7 81  1  0
  8 82  1  0
  8 83  1  0
  9 84  1  0
 10 85  1  0
 11 86  1  0
 11 87  1  0
 12 88  1  0
 13 89  1  0
 14 90  1  0
 14 91  1  0
 15 92  1  0
 16 93  1  0
 17 94  1  0
 17 95  1  0
 18 96  1  0
 18 97  1  0
 19 98  1  0
 19 99  1  0
 23100  1  1
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 28103  1  0
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 30107  1  0
 30108  1  0
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 31110  1  0
 32111  1  0
 32112  1  0
 33113  1  0
 33114  1  0
 34115  1  0
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 35118  1  0
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 39125  1  0
 39126  1  0
 40127  1  0
 40128  1  0
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 53139  1  0
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 59143  1  0
 61144  1  0
 61145  1  0
 65146  1  0
 66147  1  0
 67148  1  6
 68149  1  0
M  END
Download

PDB for HMDB0006973 (CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)))

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      34.140  -7.496   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      32.346  -8.532   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      30.551  -7.496   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      35.934  -8.532   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      28.757  -8.532   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      30.945 -10.604   0.000  0.00  0.00           O+0
HETATM    7  H   UNK     0      33.908 -10.683   0.000  0.00  0.00           H+0
HETATM    8  P   UNK     0      37.932  -7.853   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0      37.932  -9.962   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      40.407  -8.477   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      37.932  -5.946   0.000  0.00  0.00           O+0
HETATM   12  P   UNK     0      42.406  -7.798   0.000  0.00  0.00           P+0
HETATM   13  O   UNK     0      42.406  -9.907   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      44.881  -8.421   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      42.406  -5.892   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      48.539 -12.597   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      51.659 -12.597   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      53.351 -10.958   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      50.211  -9.722   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      46.573 -10.940   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      51.669 -14.090   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      48.527 -14.112   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      46.565  -9.400   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      54.611  -6.313   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      54.611  -7.853   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      53.277  -5.543   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      53.277  -8.623   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      51.944  -6.313   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      51.944  -7.853   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      53.277  -4.003   0.000  0.00  0.00           N+0
HETATM   31  O   UNK     0      55.917  -8.403   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       7.418  -8.532   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.752  -7.762   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      10.086  -8.532   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      11.419  -7.762   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      12.753  -8.532   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      14.087  -7.762   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      15.420  -8.532   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      16.754  -7.762   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      18.088  -8.532   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      19.421  -7.762   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      20.755  -8.532   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      22.089  -7.762   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      23.422  -8.532   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      24.756  -7.762   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      26.090  -8.532   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      27.423  -7.762   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0      27.423  -6.222   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0       4.272 -10.597   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       5.605 -11.368   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       6.939 -10.598   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       8.273 -11.368   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       9.606 -10.599   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      10.940 -11.369   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      12.274 -11.367   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      13.607 -10.596   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      14.941 -11.366   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      16.275 -11.370   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      17.609 -10.600   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      18.942 -11.371   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      20.276 -11.366   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      21.609 -10.595   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      22.943 -11.365   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      24.277 -11.372   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      25.611 -10.602   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      26.944 -11.372   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      28.278 -10.603   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      29.611 -11.373   0.000  0.00  0.00           C+0
HETATM   69  O   UNK     0      29.611 -12.913   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    3    6    7                                             
CONECT    3    2    5                                                       
CONECT    4    1    8                                                       
CONECT    5    3   47                                                       
CONECT    6    2   68                                                       
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   20   22                                                  
CONECT   17   16   18   21                                                  
CONECT   18   19   17   27                                                  
CONECT   19   18   20                                                       
CONECT   20   16   19   23                                                  
CONECT   21   17                                                            
CONECT   22   16                                                            
CONECT   23   20   14                                                       
CONECT   24   25   26                                                       
CONECT   25   24   27   31                                                  
CONECT   26   24   28   30                                                  
CONECT   27   25   29   18                                                  
CONECT   28   26   29                                                       
CONECT   29   27   28                                                       
CONECT   30   26                                                            
CONECT   31   25                                                            
CONECT   32   33                                                            
CONECT   33   32   34                                                       
CONECT   34   33   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    5   48                                                  
CONECT   48   47                                                            
CONECT   49   50                                                            
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   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    6   69                                                  
CONECT   69   68                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  140    0
END
Download

3D PDB for HMDB0006973 (CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)))

COMPND    HMDB0006973
HETATM    1  C1  UNL     1      -0.326  -9.845  -6.886  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.636  -9.121  -7.056  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.528  -7.785  -6.345  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.843  -7.005  -6.489  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.621  -5.684  -5.730  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.816  -4.827  -5.788  1.00  0.00           C  
HETATM    7  C7  UNL     1      -4.464  -4.428  -4.739  1.00  0.00           C  
HETATM    8  C8  UNL     1      -4.127  -4.749  -3.352  1.00  0.00           C  
HETATM    9  C9  UNL     1      -3.876  -3.543  -2.533  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.761  -3.299  -1.915  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.616  -4.249  -1.989  1.00  0.00           C  
HETATM   12  C12 UNL     1      -1.264  -4.739  -0.644  1.00  0.00           C  
HETATM   13  C13 UNL     1      -0.081  -4.585  -0.133  1.00  0.00           C  
HETATM   14  C14 UNL     1       1.091  -3.934  -0.741  1.00  0.00           C  
HETATM   15  C15 UNL     1       1.514  -2.805   0.105  1.00  0.00           C  
HETATM   16  C16 UNL     1       2.683  -2.658   0.710  1.00  0.00           C  
HETATM   17  C17 UNL     1       3.670  -3.703   0.542  1.00  0.00           C  
HETATM   18  C18 UNL     1       4.143  -4.482   1.696  1.00  0.00           C  
HETATM   19  C19 UNL     1       4.832  -3.908   2.836  1.00  0.00           C  
HETATM   20  C20 UNL     1       4.192  -2.954   3.727  1.00  0.00           C  
HETATM   21  O1  UNL     1       4.916  -2.430   4.676  1.00  0.00           O  
HETATM   22  O2  UNL     1       2.897  -2.501   3.727  1.00  0.00           O  
HETATM   23  C21 UNL     1       2.418  -1.571   4.670  1.00  0.00           C  
HETATM   24  C22 UNL     1       1.188  -1.951   5.414  1.00  0.00           C  
HETATM   25  O3  UNL     1       0.031  -2.139   4.659  1.00  0.00           O  
HETATM   26  C23 UNL     1      -0.199  -3.056   3.680  1.00  0.00           C  
HETATM   27  O4  UNL     1       0.748  -3.863   3.397  1.00  0.00           O  
HETATM   28  C24 UNL     1      -1.497  -3.158   2.934  1.00  0.00           C  
HETATM   29  C25 UNL     1      -2.393  -2.025   3.440  1.00  0.00           C  
HETATM   30  C26 UNL     1      -3.744  -2.089   2.751  1.00  0.00           C  
HETATM   31  C27 UNL     1      -4.686  -1.009   3.164  1.00  0.00           C  
HETATM   32  C28 UNL     1      -4.192   0.387   2.833  1.00  0.00           C  
HETATM   33  C29 UNL     1      -5.160   1.432   3.273  1.00  0.00           C  
HETATM   34  C30 UNL     1      -4.713   2.862   2.925  1.00  0.00           C  
HETATM   35  C31 UNL     1      -4.573   3.039   1.469  1.00  0.00           C  
HETATM   36  C32 UNL     1      -4.261   4.345   0.929  1.00  0.00           C  
HETATM   37  C33 UNL     1      -3.061   5.128   1.179  1.00  0.00           C  
HETATM   38  C34 UNL     1      -2.816   5.578   2.556  1.00  0.00           C  
HETATM   39  C35 UNL     1      -1.554   6.451   2.650  1.00  0.00           C  
HETATM   40  C36 UNL     1      -0.319   5.740   2.204  1.00  0.00           C  
HETATM   41  C37 UNL     1       0.910   6.649   2.317  1.00  0.00           C  
HETATM   42  C38 UNL     1       2.098   5.847   1.843  1.00  0.00           C  
HETATM   43  C39 UNL     1       2.119  -0.229   3.961  1.00  0.00           C  
HETATM   44  O5  UNL     1       1.168  -0.470   2.998  1.00  0.00           O  
HETATM   45  P1  UNL     1       0.763   0.947   2.154  1.00  0.00           P  
HETATM   46  O6  UNL     1      -0.680   1.267   2.436  1.00  0.00           O  
HETATM   47  O7  UNL     1       1.740   2.212   2.766  1.00  0.00           O  
HETATM   48  O8  UNL     1       1.035   0.704   0.526  1.00  0.00           O  
HETATM   49  P2  UNL     1      -0.220   1.288  -0.436  1.00  0.00           P  
HETATM   50  O9  UNL     1      -1.173   2.053   0.467  1.00  0.00           O  
HETATM   51  O10 UNL     1      -1.031   0.019  -1.214  1.00  0.00           O  
HETATM   52  O11 UNL     1       0.351   2.320  -1.623  1.00  0.00           O  
HETATM   53  C40 UNL     1       1.183   1.676  -2.537  1.00  0.00           C  
HETATM   54  C41 UNL     1       1.606   2.729  -3.535  1.00  0.00           C  
HETATM   55  O12 UNL     1       2.281   3.727  -2.853  1.00  0.00           O  
HETATM   56  C42 UNL     1       3.243   4.230  -3.723  1.00  0.00           C  
HETATM   57  N1  UNL     1       4.295   4.955  -3.050  1.00  0.00           N  
HETATM   58  C43 UNL     1       5.042   5.864  -3.702  1.00  0.00           C  
HETATM   59  C44 UNL     1       6.055   6.577  -3.089  1.00  0.00           C  
HETATM   60  C45 UNL     1       6.327   6.363  -1.754  1.00  0.00           C  
HETATM   61  N2  UNL     1       7.369   7.080  -1.070  1.00  0.00           N  
HETATM   62  N3  UNL     1       5.568   5.448  -1.117  1.00  0.00           N  
HETATM   63  C46 UNL     1       4.579   4.765  -1.752  1.00  0.00           C  
HETATM   64  O13 UNL     1       3.927   3.928  -1.060  1.00  0.00           O  
HETATM   65  C47 UNL     1       3.737   3.051  -4.527  1.00  0.00           C  
HETATM   66  O14 UNL     1       4.748   2.351  -3.888  1.00  0.00           O  
HETATM   67  C48 UNL     1       2.468   2.226  -4.633  1.00  0.00           C  
HETATM   68  O15 UNL     1       2.716   0.872  -4.593  1.00  0.00           O  
HETATM   69  H1  UNL     1       0.505  -9.189  -7.177  1.00  0.00           H  
HETATM   70  H2  UNL     1      -0.217 -10.056  -5.788  1.00  0.00           H  
HETATM   71  H3  UNL     1      -0.318 -10.820  -7.419  1.00  0.00           H  
HETATM   72  H4  UNL     1      -2.476  -9.683  -6.586  1.00  0.00           H  
HETATM   73  H5  UNL     1      -1.811  -8.973  -8.135  1.00  0.00           H  
HETATM   74  H6  UNL     1      -1.346  -7.990  -5.271  1.00  0.00           H  
HETATM   75  H7  UNL     1      -0.706  -7.180  -6.800  1.00  0.00           H  
HETATM   76  H8  UNL     1      -3.024  -6.738  -7.530  1.00  0.00           H  
HETATM   77  H9  UNL     1      -3.653  -7.589  -6.030  1.00  0.00           H  
HETATM   78  H10 UNL     1      -1.833  -5.155  -6.342  1.00  0.00           H  
HETATM   79  H11 UNL     1      -2.219  -5.916  -4.753  1.00  0.00           H  
HETATM   80  H12 UNL     1      -4.143  -4.532  -6.817  1.00  0.00           H  
HETATM   81  H13 UNL     1      -5.346  -3.788  -4.924  1.00  0.00           H  
HETATM   82  H14 UNL     1      -5.093  -5.184  -2.861  1.00  0.00           H  
HETATM   83  H15 UNL     1      -3.434  -5.572  -3.244  1.00  0.00           H  
HETATM   84  H16 UNL     1      -4.743  -2.839  -2.486  1.00  0.00           H  
HETATM   85  H17 UNL     1      -2.654  -2.369  -1.322  1.00  0.00           H  
HETATM   86  H18 UNL     1      -0.772  -3.597  -2.362  1.00  0.00           H  
HETATM   87  H19 UNL     1      -1.744  -5.038  -2.717  1.00  0.00           H  
HETATM   88  H20 UNL     1      -2.034  -5.262  -0.037  1.00  0.00           H  
HETATM   89  H21 UNL     1       0.099  -4.986   0.889  1.00  0.00           H  
HETATM   90  H22 UNL     1       0.822  -3.486  -1.713  1.00  0.00           H  
HETATM   91  H23 UNL     1       1.881  -4.672  -0.997  1.00  0.00           H  
HETATM   92  H24 UNL     1       0.776  -1.997   0.249  1.00  0.00           H  
HETATM   93  H25 UNL     1       2.918  -1.764   1.289  1.00  0.00           H  
HETATM   94  H26 UNL     1       4.616  -3.124   0.145  1.00  0.00           H  
HETATM   95  H27 UNL     1       3.525  -4.407  -0.302  1.00  0.00           H  
HETATM   96  H28 UNL     1       4.735  -5.370   1.257  1.00  0.00           H  
HETATM   97  H29 UNL     1       3.243  -5.066   2.123  1.00  0.00           H  
HETATM   98  H30 UNL     1       5.845  -3.461   2.576  1.00  0.00           H  
HETATM   99  H31 UNL     1       5.176  -4.799   3.486  1.00  0.00           H  
HETATM  100  H32 UNL     1       3.256  -1.362   5.407  1.00  0.00           H  
HETATM  101  H33 UNL     1       1.016  -1.124   6.172  1.00  0.00           H  
HETATM  102  H34 UNL     1       1.410  -2.856   6.037  1.00  0.00           H  
HETATM  103  H35 UNL     1      -1.246  -2.887   1.870  1.00  0.00           H  
HETATM  104  H36 UNL     1      -1.957  -4.139   3.007  1.00  0.00           H  
HETATM  105  H37 UNL     1      -2.522  -2.056   4.526  1.00  0.00           H  
HETATM  106  H38 UNL     1      -1.911  -1.086   3.108  1.00  0.00           H  
HETATM  107  H39 UNL     1      -3.599  -2.042   1.635  1.00  0.00           H  
HETATM  108  H40 UNL     1      -4.203  -3.078   2.968  1.00  0.00           H  
HETATM  109  H41 UNL     1      -5.666  -1.113   2.645  1.00  0.00           H  
HETATM  110  H42 UNL     1      -4.865  -1.062   4.258  1.00  0.00           H  
HETATM  111  H43 UNL     1      -4.136   0.398   1.703  1.00  0.00           H  
HETATM  112  H44 UNL     1      -3.219   0.531   3.311  1.00  0.00           H  
HETATM  113  H45 UNL     1      -6.173   1.293   2.873  1.00  0.00           H  
HETATM  114  H46 UNL     1      -5.221   1.404   4.384  1.00  0.00           H  
HETATM  115  H47 UNL     1      -5.493   3.531   3.322  1.00  0.00           H  
HETATM  116  H48 UNL     1      -3.789   3.017   3.520  1.00  0.00           H  
HETATM  117  H49 UNL     1      -5.565   2.713   1.005  1.00  0.00           H  
HETATM  118  H50 UNL     1      -3.849   2.273   1.029  1.00  0.00           H  
HETATM  119  H51 UNL     1      -4.331   4.220  -0.230  1.00  0.00           H  
HETATM  120  H52 UNL     1      -5.200   5.042   1.052  1.00  0.00           H  
HETATM  121  H53 UNL     1      -2.157   4.603   0.729  1.00  0.00           H  
HETATM  122  H54 UNL     1      -3.071   6.093   0.545  1.00  0.00           H  
HETATM  123  H55 UNL     1      -2.758   4.860   3.361  1.00  0.00           H  
HETATM  124  H56 UNL     1      -3.647   6.296   2.830  1.00  0.00           H  
HETATM  125  H57 UNL     1      -1.699   7.413   2.125  1.00  0.00           H  
HETATM  126  H58 UNL     1      -1.448   6.691   3.738  1.00  0.00           H  
HETATM  127  H59 UNL     1      -0.118   4.846   2.817  1.00  0.00           H  
HETATM  128  H60 UNL     1      -0.391   5.517   1.106  1.00  0.00           H  
HETATM  129  H61 UNL     1       1.084   6.941   3.368  1.00  0.00           H  
HETATM  130  H62 UNL     1       0.778   7.565   1.692  1.00  0.00           H  
HETATM  131  H63 UNL     1       3.061   6.394   2.037  1.00  0.00           H  
HETATM  132  H64 UNL     1       2.080   4.895   2.410  1.00  0.00           H  
HETATM  133  H65 UNL     1       2.021   5.664   0.743  1.00  0.00           H  
HETATM  134  H66 UNL     1       3.041   0.239   3.596  1.00  0.00           H  
HETATM  135  H67 UNL     1       1.682   0.423   4.735  1.00  0.00           H  
HETATM  136  H68 UNL     1       1.512   2.350   3.719  1.00  0.00           H  
HETATM  137  H69 UNL     1      -1.472   0.407  -2.007  1.00  0.00           H  
HETATM  138  H70 UNL     1       0.596   0.864  -3.015  1.00  0.00           H  
HETATM  139  H71 UNL     1       2.114   1.299  -2.060  1.00  0.00           H  
HETATM  140  H72 UNL     1       0.657   3.208  -3.913  1.00  0.00           H  
HETATM  141  H73 UNL     1       2.687   4.883  -4.450  1.00  0.00           H  
HETATM  142  H74 UNL     1       4.810   6.015  -4.747  1.00  0.00           H  
HETATM  143  H75 UNL     1       6.660   7.309  -3.605  1.00  0.00           H  
HETATM  144  H76 UNL     1       7.300   7.296  -0.039  1.00  0.00           H  
HETATM  145  H77 UNL     1       8.217   7.408  -1.556  1.00  0.00           H  
HETATM  146  H78 UNL     1       4.092   3.338  -5.537  1.00  0.00           H  
HETATM  147  H79 UNL     1       4.328   1.539  -3.488  1.00  0.00           H  
HETATM  148  H80 UNL     1       1.987   2.540  -5.606  1.00  0.00           H  
HETATM  149  H81 UNL     1       1.845   0.410  -4.714  1.00  0.00           H  
CONECT    1    2   69   70   71
CONECT    2    3   72   73
CONECT    3    4   74   75
CONECT    4    5   76   77
CONECT    5    6   78   79
CONECT    6    7    7   80
CONECT    7    8   81
CONECT    8    9   82   83
CONECT    9   10   10   84
CONECT   10   11   85
CONECT   11   12   86   87
CONECT   12   13   13   88
CONECT   13   14   89
CONECT   14   15   90   91
CONECT   15   16   16   92
CONECT   16   17   93
CONECT   17   18   94   95
CONECT   18   19   96   97
CONECT   19   20   98   99
CONECT   20   21   21   22
CONECT   22   23
CONECT   23   24   43  100
CONECT   24   25  101  102
CONECT   25   26
CONECT   26   27   27   28
CONECT   28   29  103  104
CONECT   29   30  105  106
CONECT   30   31  107  108
CONECT   31   32  109  110
CONECT   32   33  111  112
CONECT   33   34  113  114
CONECT   34   35  115  116
CONECT   35   36  117  118
CONECT   36   37  119  120
CONECT   37   38  121  122
CONECT   38   39  123  124
CONECT   39   40  125  126
CONECT   40   41  127  128
CONECT   41   42  129  130
CONECT   42  131  132  133
CONECT   43   44  134  135
CONECT   44   45
CONECT   45   46   46   47   48
CONECT   47  136
CONECT   48   49
CONECT   49   50   50   51   52
CONECT   51  137
CONECT   52   53
CONECT   53   54  138  139
CONECT   54   55   67  140
CONECT   55   56
CONECT   56   57   65  141
CONECT   57   58   63
CONECT   58   59   59  142
CONECT   59   60  143
CONECT   60   61   62   62
CONECT   61  144  145
CONECT   62   63
CONECT   63   64   64
CONECT   65   66   67  146
CONECT   66  147
CONECT   67   68  148
CONECT   68  149
END
Download

SMILES for HMDB0006973 (CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)))

[H][C@@](COC(=O)CCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC
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INCHI for HMDB0006973 (CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)))

InChI=1S/C48H81N3O15P2/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-44(53)64-40(37-61-43(52)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2)38-62-67(57,58)66-68(59,60)63-39-41-45(54)46(55)47(65-41)51-36-35-42(49)50-48(51)56/h11,13,17-18,20,22,26,28,35-36,40-41,45-47,54-55H,3-10,12,14-16,19,21,23-25,27,29-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b13-11-,18-17-,22-20-,28-26-/t40-,41-,45+,46?,47-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-CDPHMDB
1-Palmitoyl-2-arachidonoyl-sn-glycero-3-cytidine-5'-diphosphateHMDB
CDP-DG(16:0/20:4)HMDB
CDP-DG(16:0/20:4N6)HMDB
CDP-DG(16:0/20:4W6)HMDB
CDP-DG(36:4)HMDB
CDP-Diacylglycerol(16:0/20:4)HMDB
CDP-Diacylglycerol(16:0/20:4N6)HMDB
CDP-Diacylglycerol(16:0/20:4W6)HMDB
CDP-Diacylglycerol(36:4)HMDB
Chemical FormulaC48H81N3O15P2
Average Molecular Weight1002.1154
Monoisotopic Molecular Weight1001.514291961
IUPAC Name[({[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(2R)-3-(hexadecanoyloxy)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxy]phosphinic acid
Traditional Name{[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(2R)-3-(hexadecanoyloxy)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoyloxy]propoxyphosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC
InChI Identifier
InChI=1S/C48H81N3O15P2/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-44(53)64-40(37-61-43(52)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2)38-62-67(57,58)66-68(59,60)63-39-41-45(54)46(55)47(65-41)51-36-35-42(49)50-48(51)56/h11,13,17-18,20,22,26,28,35-36,40-41,45-47,54-55H,3-10,12,14-16,19,21,23-25,27,29-34,37-39H2,1-2H3,(H,57,58)(H,59,60)(H2,49,50,56)/b13-11-,18-17-,22-20-,28-26-/t40-,41-,45+,46?,47-/m1/s1
InChI KeyGMBXECXXNMMIAN-HUOFUYQBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha-hydroxy ketones. These are organic compounds containing a carboxylic acid, and an amine group attached to the alpha carbon atom, relative to the C=O group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentAlpha-hydroxy ketones
Alternative Parents
Substituents
  • Alpha-hydroxy ketone
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
Water Solubility0.0026 g/LALOGPS
logP6.86ALOGPS
logP9.61ChemAxon
logS-5.6ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.52ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area263.27 ŲChemAxon
Rotatable Bond Count42ChemAxon
Refractivity263.08 m³·mol⁻¹ChemAxon
Polarizability108.52 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]+275.10230932474
DeepCCS[M-H]-273.27730932474
DeepCCS[M-2H]-306.51530932474
DeepCCS[M+Na]+280.70730932474
AllCCS[M+H]+311.132859911
AllCCS[M+H-H2O]+311.532859911
AllCCS[M+NH4]+310.732859911
AllCCS[M+Na]+310.532859911
AllCCS[M-H]-296.032859911
AllCCS[M+Na-2H]-302.932859911
AllCCS[M+HCOO]-310.332859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 10V, Positive-QTOFsplash10-03di-0920000100-63b7b84a7ff237c3f3302017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 20V, Positive-QTOFsplash10-03di-1920001000-a251848f8c1d4b9fe5912017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 40V, Positive-QTOFsplash10-03di-3930000000-d90494fc2c957b8153862017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 10V, Negative-QTOFsplash10-0a4i-1892001202-244b3467b3621b9b21f62017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 20V, Negative-QTOFsplash10-0bt9-5692110201-05b4d9d35b9e18df0d7a2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 40V, Negative-QTOFsplash10-0a4i-5911000000-c6294693bf454b2db7ea2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 10V, Negative-QTOFsplash10-0udi-9000002001-753fc5cb6ecbffc5592f2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 20V, Negative-QTOFsplash10-054x-9062703100-da0a5a0aaee0ce9e69c32021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 40V, Negative-QTOFsplash10-0a59-9347200101-5ceafba4725d52f31a942021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 10V, Positive-QTOFsplash10-0udi-9000000033-8b5c4976b1e73c1b02012021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 20V, Positive-QTOFsplash10-0lxx-5000000059-62a82bf36200380ee6942021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(16:0/20:4(5Z,8Z,11Z,14Z)) 40V, Positive-QTOFsplash10-006x-0259733002-3c86197eedd14e426dc12021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue Locations
  • All Tissues
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 IDFDB024167
KNApSAcK IDNot Available
Chemspider ID24765813
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53477917
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

Enzymes

Enzyme Details
1. Phosphatidate cytidylyltransferase 2
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
Provides CDP-diacylglycerol an important precursor for the synthesis of phosphatidylinositol, phosphatidylglycerol, and cardiolipin.
Gene Name:
CDS2
Uniprot ID:
O95674
Molecular weight:
51417.5
Enzyme Details
2. Phosphatidate cytidylyltransferase 1
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
Provides CDP-diacylglycerol an important precursor for the synthesis of phosphatidylinositol (PtdIns), phosphatidylglycerol, and cardiolipin. Overexpression may amplify cellular signaling responses from cytokines. May also play an important role in the signal transduction mechanism of retina and neural cells.
Gene Name:
CDS1
Uniprot ID:
Q92903
Molecular weight:
53303.57
Enzyme Details
3. CDP-diacylglycerol--inositol 3-phosphatidyltransferase
General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
Catalyzes the biosynthesis of phosphatidylinositol (PtdIns) as well as PtdIns:inositol exchange reaction. May thus act to reduce an excessive cellular PtdIns content. The exchange activity is due to the reverse reaction of PtdIns synthase and is dependent on CMP, which is tightly bound to the enzyme.
Gene Name:
CDIPT
Uniprot ID:
O14735
Molecular weight:
23538.47
Enzyme Details
4. CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin (By similarity).
Gene Name:
PGS1
Uniprot ID:
Q32NB8
Molecular weight:
62729.745