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Showing metabocard for CDP-DG(i-12:0/i-20:0) (HMDB0116165)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 07:17:31 UTC
Update Date2022-11-30 19:26:29 UTC
HMDB IDHMDB0116165
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(i-12:0/i-20:0)
DescriptionCDP-DG(i-12:0/i-20:0) 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-12:0/i-20:0), in particular, consists of one chain of isododecanoic acid at the C-1 position and one chain of isoeicosanoic 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?1563873681
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116165 (CDP-DG(i-12:0/i-20:0))

CDP-DG(i-12:0/i-20:0)
  Mrv1652309161722312D          

 65 66  0  0  1  0            999 V2000
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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
Download

3D MOL for HMDB0116165 (CDP-DG(i-12:0/i-20:0))

HMDB0116165
     RDKit          3D
CDP-DG(i-12:0/i-20:0)
145146  0  0  0  0  0  0  0  0999 V2000
    0.0095    5.3505   -6.1129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0475    3.9079   -5.7145 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3444    3.3398   -5.4955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7422    3.0400   -6.7639 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7193    1.6305   -6.2215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3704    0.6278   -7.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2406   -0.7372   -6.4003 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.8961   -3.1457   -6.6268 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.8363    2.2632    4.9726 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116165 (CDP-DG(i-12:0/i-20:0))

CDP-DG(i-12:0/i-20:0)
  Mrv1652309161722312D          

 65 66  0  0  1  0            999 V2000
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   16.4838   -4.5706    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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 63 65  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0116165

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CCCCCCCCC(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)CCCCCCCCCCCCCCCCC(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C44H81N3O15P2/c1-34(2)25-21-17-13-11-9-7-5-6-8-10-12-14-20-24-28-40(49)60-36(31-57-39(48)27-23-19-16-15-18-22-26-35(3)4)32-58-63(53,54)62-64(55,56)59-33-37-41(50)42(51)43(61-37)47-30-29-38(45)46-44(47)52/h29-30,34-37,41-43,50-51H,5-28,31-33H2,1-4H3,(H,53,54)(H,55,56)(H2,45,46,52)/t36-,37-,41+,42?,43-/m1/s1

> <INCHI_KEY>
BGBQRMYUYXUIPR-QDFYKRCGSA-N

> <FORMULA>
C44H81N3O15P2

> <MOLECULAR_WEIGHT>
954.086

> <EXACT_MASS>
953.514292916

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
145

> <JCHEM_AVERAGE_POLARIZABILITY>
105.39768291695562

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-2-[(18-methylnonadecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
5.70

> <JCHEM_LOGP>
9.241650641333335

> <ALOGPS_LOGS>
-5.13

> <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>
240.10570000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
40

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.05e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-2-[(18-methylnonadecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116165 (CDP-DG(i-12:0/i-20:0))

HMDB0116165
     RDKit          3D
CDP-DG(i-12:0/i-20:0)
145146  0  0  0  0  0  0  0  0999 V2000
    0.0095    5.3505   -6.1129 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.7193    1.6305   -6.2215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3704    0.6278   -7.1543 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2406   -0.7372   -6.4003 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.8961   -3.1457   -6.6268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7404   -3.9265   -6.1781 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0906   -3.4186   -5.0510 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1885   -4.4395   -4.7104 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6573   -0.8098    2.6631 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5360   -0.6016    1.6412 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.4763    1.1893    7.0066 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.5713    0.8777    6.8391 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6568    3.3766    6.3358 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
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PDB for HMDB0116165 (CDP-DG(i-12:0/i-20:0))

HEADER    PROTEIN                                 16-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(i-12:0/i-20:0)                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-SEP-17         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      12.517  -9.302   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      28.036 -11.374   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      28.036 -12.814   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0      26.703 -10.603   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      25.370 -11.374   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      24.037 -10.603   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      22.704 -11.374   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      21.371 -10.603   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      20.038 -11.374   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      18.705 -10.603   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      17.372 -11.374   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      16.038 -10.603   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      14.705 -11.374   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      13.372 -10.603   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      12.039 -11.374   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      10.706 -10.603   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       9.373 -11.374   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       8.040 -10.603   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       6.707 -11.374   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       5.374 -10.603   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0       4.041 -11.374   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0       4.041  -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   45                                                       
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   44                                                  
CONECT   43   42                                                            
CONECT   44   42                                                            
CONECT   45    6   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45   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   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   65                                                  
CONECT   64   63                                                            
CONECT   65   63                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  132    0
END
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3D PDB for HMDB0116165 (CDP-DG(i-12:0/i-20:0))

COMPND    HMDB0116165
HETATM    1  C1  UNL     1       0.009   5.351  -6.113  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.047   3.908  -5.715  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.344   3.340  -5.496  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.742   3.040  -6.764  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.719   1.631  -6.222  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.370   0.628  -7.154  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.241  -0.737  -6.400  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.828  -1.815  -7.219  1.00  0.00           C  
HETATM    9  C9  UNL     1      -1.896  -3.146  -6.627  1.00  0.00           C  
HETATM   10  C10 UNL     1      -0.740  -3.927  -6.178  1.00  0.00           C  
HETATM   11  C11 UNL     1       0.091  -3.419  -5.051  1.00  0.00           C  
HETATM   12  C12 UNL     1       1.189  -4.440  -4.710  1.00  0.00           C  
HETATM   13  C13 UNL     1       2.017  -3.955  -3.553  1.00  0.00           C  
HETATM   14  C14 UNL     1       2.745  -2.663  -3.844  1.00  0.00           C  
HETATM   15  C15 UNL     1       3.510  -2.193  -2.648  1.00  0.00           C  
HETATM   16  C16 UNL     1       4.569  -3.155  -2.146  1.00  0.00           C  
HETATM   17  C17 UNL     1       5.159  -2.461  -0.924  1.00  0.00           C  
HETATM   18  C18 UNL     1       6.231  -3.226  -0.227  1.00  0.00           C  
HETATM   19  C19 UNL     1       6.698  -2.426   1.002  1.00  0.00           C  
HETATM   20  C20 UNL     1       5.472  -2.245   1.853  1.00  0.00           C  
HETATM   21  O1  UNL     1       4.994  -3.167   2.541  1.00  0.00           O  
HETATM   22  O2  UNL     1       4.810  -1.033   1.908  1.00  0.00           O  
HETATM   23  C21 UNL     1       3.657  -0.810   2.663  1.00  0.00           C  
HETATM   24  C22 UNL     1       2.536  -0.602   1.641  1.00  0.00           C  
HETATM   25  O3  UNL     1       1.281  -0.351   2.262  1.00  0.00           O  
HETATM   26  C23 UNL     1       0.195  -0.139   1.440  1.00  0.00           C  
HETATM   27  O4  UNL     1       0.322  -0.167   0.207  1.00  0.00           O  
HETATM   28  C24 UNL     1      -1.138   0.126   2.035  1.00  0.00           C  
HETATM   29  C25 UNL     1      -2.171   0.372   0.986  1.00  0.00           C  
HETATM   30  C26 UNL     1      -3.529   0.593   1.485  1.00  0.00           C  
HETATM   31  C27 UNL     1      -4.432  -0.449   1.973  1.00  0.00           C  
HETATM   32  C28 UNL     1      -4.095  -1.483   2.933  1.00  0.00           C  
HETATM   33  C29 UNL     1      -3.256  -2.648   2.367  1.00  0.00           C  
HETATM   34  C30 UNL     1      -2.908  -3.560   3.473  1.00  0.00           C  
HETATM   35  C31 UNL     1      -2.176  -4.788   3.163  1.00  0.00           C  
HETATM   36  C32 UNL     1      -0.842  -4.622   2.538  1.00  0.00           C  
HETATM   37  C33 UNL     1      -0.779  -3.984   1.202  1.00  0.00           C  
HETATM   38  C34 UNL     1      -0.101  -5.974   2.468  1.00  0.00           C  
HETATM   39  C35 UNL     1       3.641   0.334   3.587  1.00  0.00           C  
HETATM   40  O5  UNL     1       4.581   0.354   4.584  1.00  0.00           O  
HETATM   41  P1  UNL     1       4.460   1.699   5.578  1.00  0.00           P  
HETATM   42  O6  UNL     1       4.476   1.189   7.007  1.00  0.00           O  
HETATM   43  O7  UNL     1       5.839   2.649   5.363  1.00  0.00           O  
HETATM   44  O8  UNL     1       3.093   2.641   5.265  1.00  0.00           O  
HETATM   45  P2  UNL     1       2.071   2.494   6.584  1.00  0.00           P  
HETATM   46  O9  UNL     1       2.750   2.916   7.883  1.00  0.00           O  
HETATM   47  O10 UNL     1       1.571   0.878   6.839  1.00  0.00           O  
HETATM   48  O11 UNL     1       0.657   3.377   6.336  1.00  0.00           O  
HETATM   49  C36 UNL     1       0.484   3.697   4.992  1.00  0.00           C  
HETATM   50  C37 UNL     1      -0.824   4.464   4.923  1.00  0.00           C  
HETATM   51  O12 UNL     1      -1.163   4.857   3.632  1.00  0.00           O  
HETATM   52  C38 UNL     1      -2.470   5.347   3.843  1.00  0.00           C  
HETATM   53  N1  UNL     1      -3.072   5.773   2.603  1.00  0.00           N  
HETATM   54  C39 UNL     1      -3.477   4.973   1.630  1.00  0.00           C  
HETATM   55  C40 UNL     1      -4.053   5.465   0.458  1.00  0.00           C  
HETATM   56  C41 UNL     1      -4.210   6.833   0.300  1.00  0.00           C  
HETATM   57  N2  UNL     1      -4.794   7.368  -0.885  1.00  0.00           N  
HETATM   58  N3  UNL     1      -3.787   7.614   1.310  1.00  0.00           N  
HETATM   59  C42 UNL     1      -3.237   7.114   2.426  1.00  0.00           C  
HETATM   60  O13 UNL     1      -2.873   7.923   3.312  1.00  0.00           O  
HETATM   61  C43 UNL     1      -3.139   4.156   4.474  1.00  0.00           C  
HETATM   62  O14 UNL     1      -4.187   4.504   5.336  1.00  0.00           O  
HETATM   63  C44 UNL     1      -1.989   3.598   5.309  1.00  0.00           C  
HETATM   64  O15 UNL     1      -1.836   2.263   4.973  1.00  0.00           O  
HETATM   65  H1  UNL     1      -1.008   5.689  -6.400  1.00  0.00           H  
HETATM   66  H2  UNL     1       0.722   5.462  -6.948  1.00  0.00           H  
HETATM   67  H3  UNL     1       0.359   5.909  -5.199  1.00  0.00           H  
HETATM   68  H4  UNL     1      -0.613   3.742  -4.767  1.00  0.00           H  
HETATM   69  H5  UNL     1       2.079   4.169  -5.316  1.00  0.00           H  
HETATM   70  H6  UNL     1       1.367   2.685  -4.606  1.00  0.00           H  
HETATM   71  H7  UNL     1       1.666   2.807  -6.421  1.00  0.00           H  
HETATM   72  H8  UNL     1      -1.762   3.396  -6.966  1.00  0.00           H  
HETATM   73  H9  UNL     1      -0.137   3.117  -7.684  1.00  0.00           H  
HETATM   74  H10 UNL     1       0.334   1.292  -6.089  1.00  0.00           H  
HETATM   75  H11 UNL     1      -1.297   1.632  -5.277  1.00  0.00           H  
HETATM   76  H12 UNL     1      -2.444   0.839  -7.314  1.00  0.00           H  
HETATM   77  H13 UNL     1      -0.885   0.580  -8.133  1.00  0.00           H  
HETATM   78  H14 UNL     1      -1.677  -0.567  -5.415  1.00  0.00           H  
HETATM   79  H15 UNL     1      -0.128  -0.800  -6.289  1.00  0.00           H  
HETATM   80  H16 UNL     1      -2.821  -1.501  -7.670  1.00  0.00           H  
HETATM   81  H17 UNL     1      -1.175  -1.907  -8.158  1.00  0.00           H  
HETATM   82  H18 UNL     1      -2.608  -3.126  -5.699  1.00  0.00           H  
HETATM   83  H19 UNL     1      -2.573  -3.800  -7.312  1.00  0.00           H  
HETATM   84  H20 UNL     1      -0.032  -4.016  -7.069  1.00  0.00           H  
HETATM   85  H21 UNL     1      -1.066  -4.994  -5.983  1.00  0.00           H  
HETATM   86  H22 UNL     1      -0.587  -3.364  -4.151  1.00  0.00           H  
HETATM   87  H23 UNL     1       0.583  -2.463  -5.230  1.00  0.00           H  
HETATM   88  H24 UNL     1       1.832  -4.554  -5.599  1.00  0.00           H  
HETATM   89  H25 UNL     1       0.752  -5.408  -4.436  1.00  0.00           H  
HETATM   90  H26 UNL     1       2.806  -4.692  -3.273  1.00  0.00           H  
HETATM   91  H27 UNL     1       1.347  -3.869  -2.680  1.00  0.00           H  
HETATM   92  H28 UNL     1       1.989  -1.885  -4.058  1.00  0.00           H  
HETATM   93  H29 UNL     1       3.463  -2.811  -4.687  1.00  0.00           H  
HETATM   94  H30 UNL     1       4.022  -1.218  -2.847  1.00  0.00           H  
HETATM   95  H31 UNL     1       2.756  -1.972  -1.858  1.00  0.00           H  
HETATM   96  H32 UNL     1       4.133  -4.125  -1.815  1.00  0.00           H  
HETATM   97  H33 UNL     1       5.372  -3.274  -2.879  1.00  0.00           H  
HETATM   98  H34 UNL     1       4.303  -2.208  -0.279  1.00  0.00           H  
HETATM   99  H35 UNL     1       5.632  -1.525  -1.356  1.00  0.00           H  
HETATM  100  H36 UNL     1       7.104  -3.448  -0.845  1.00  0.00           H  
HETATM  101  H37 UNL     1       5.851  -4.188   0.170  1.00  0.00           H  
HETATM  102  H38 UNL     1       7.107  -1.474   0.645  1.00  0.00           H  
HETATM  103  H39 UNL     1       7.417  -3.027   1.564  1.00  0.00           H  
HETATM  104  H40 UNL     1       3.401  -1.752   3.180  1.00  0.00           H  
HETATM  105  H41 UNL     1       2.816   0.207   0.944  1.00  0.00           H  
HETATM  106  H42 UNL     1       2.412  -1.525   1.001  1.00  0.00           H  
HETATM  107  H43 UNL     1      -1.029   1.149   2.584  1.00  0.00           H  
HETATM  108  H44 UNL     1      -1.398  -0.610   2.772  1.00  0.00           H  
HETATM  109  H45 UNL     1      -2.119  -0.410   0.168  1.00  0.00           H  
HETATM  110  H46 UNL     1      -1.834   1.305   0.425  1.00  0.00           H  
HETATM  111  H47 UNL     1      -4.147   1.195   0.700  1.00  0.00           H  
HETATM  112  H48 UNL     1      -3.497   1.416   2.313  1.00  0.00           H  
HETATM  113  H49 UNL     1      -5.416   0.033   2.347  1.00  0.00           H  
HETATM  114  H50 UNL     1      -4.877  -0.982   1.024  1.00  0.00           H  
HETATM  115  H51 UNL     1      -4.989  -1.941   3.440  1.00  0.00           H  
HETATM  116  H52 UNL     1      -3.495  -1.043   3.782  1.00  0.00           H  
HETATM  117  H53 UNL     1      -4.003  -3.233   1.712  1.00  0.00           H  
HETATM  118  H54 UNL     1      -2.473  -2.247   1.776  1.00  0.00           H  
HETATM  119  H55 UNL     1      -2.398  -2.968   4.316  1.00  0.00           H  
HETATM  120  H56 UNL     1      -3.899  -3.861   3.967  1.00  0.00           H  
HETATM  121  H57 UNL     1      -2.832  -5.460   2.493  1.00  0.00           H  
HETATM  122  H58 UNL     1      -2.020  -5.437   4.099  1.00  0.00           H  
HETATM  123  H59 UNL     1      -0.203  -4.041   3.278  1.00  0.00           H  
HETATM  124  H60 UNL     1      -0.033  -4.595   0.590  1.00  0.00           H  
HETATM  125  H61 UNL     1      -1.758  -4.095   0.691  1.00  0.00           H  
HETATM  126  H62 UNL     1      -0.413  -2.943   1.251  1.00  0.00           H  
HETATM  127  H63 UNL     1      -0.119  -6.472   3.448  1.00  0.00           H  
HETATM  128  H64 UNL     1       0.945  -5.724   2.207  1.00  0.00           H  
HETATM  129  H65 UNL     1      -0.580  -6.568   1.663  1.00  0.00           H  
HETATM  130  H66 UNL     1       3.654   1.315   3.064  1.00  0.00           H  
HETATM  131  H67 UNL     1       2.636   0.306   4.107  1.00  0.00           H  
HETATM  132  H68 UNL     1       5.644   3.610   5.529  1.00  0.00           H  
HETATM  133  H69 UNL     1       2.275   0.455   7.381  1.00  0.00           H  
HETATM  134  H70 UNL     1       0.507   2.848   4.313  1.00  0.00           H  
HETATM  135  H71 UNL     1       1.316   4.383   4.735  1.00  0.00           H  
HETATM  136  H72 UNL     1      -0.819   5.354   5.559  1.00  0.00           H  
HETATM  137  H73 UNL     1      -2.387   6.177   4.573  1.00  0.00           H  
HETATM  138  H74 UNL     1      -3.357   3.907   1.747  1.00  0.00           H  
HETATM  139  H75 UNL     1      -4.383   4.805  -0.330  1.00  0.00           H  
HETATM  140  H76 UNL     1      -4.317   8.107  -1.430  1.00  0.00           H  
HETATM  141  H77 UNL     1      -5.715   7.009  -1.203  1.00  0.00           H  
HETATM  142  H78 UNL     1      -3.462   3.427   3.712  1.00  0.00           H  
HETATM  143  H79 UNL     1      -5.022   4.381   4.849  1.00  0.00           H  
HETATM  144  H80 UNL     1      -2.162   3.740   6.397  1.00  0.00           H  
HETATM  145  H81 UNL     1      -1.600   1.675   5.737  1.00  0.00           H  
CONECT    1    2   65   66   67
CONECT    2    3    4   68
CONECT    3   69   70   71
CONECT    4    5   72   73
CONECT    5    6   74   75
CONECT    6    7   76   77
CONECT    7    8   78   79
CONECT    8    9   80   81
CONECT    9   10   82   83
CONECT   10   11   84   85
CONECT   11   12   86   87
CONECT   12   13   88   89
CONECT   13   14   90   91
CONECT   14   15   92   93
CONECT   15   16   94   95
CONECT   16   17   96   97
CONECT   17   18   98   99
CONECT   18   19  100  101
CONECT   19   20  102  103
CONECT   20   21   21   22
CONECT   22   23
CONECT   23   24   39  104
CONECT   24   25  105  106
CONECT   25   26
CONECT   26   27   27   28
CONECT   28   29  107  108
CONECT   29   30  109  110
CONECT   30   31  111  112
CONECT   31   32  113  114
CONECT   32   33  115  116
CONECT   33   34  117  118
CONECT   34   35  119  120
CONECT   35   36  121  122
CONECT   36   37   38  123
CONECT   37  124  125  126
CONECT   38  127  128  129
CONECT   39   40  130  131
CONECT   40   41
CONECT   41   42   42   43   44
CONECT   43  132
CONECT   44   45
CONECT   45   46   46   47   48
CONECT   47  133
CONECT   48   49
CONECT   49   50  134  135
CONECT   50   51   63  136
CONECT   51   52
CONECT   52   53   61  137
CONECT   53   54   59
CONECT   54   55   55  138
CONECT   55   56  139
CONECT   56   57   58   58
CONECT   57  140  141
CONECT   58   59
CONECT   59   60   60
CONECT   61   62   63  142
CONECT   62  143
CONECT   63   64  144
CONECT   64  145
END
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SMILES for HMDB0116165 (CDP-DG(i-12:0/i-20:0))

[H][C@@](COC(=O)CCCCCCCCC(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)CCCCCCCCCCCCCCCCC(C)C
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INCHI for HMDB0116165 (CDP-DG(i-12:0/i-20:0))

InChI=1S/C44H81N3O15P2/c1-34(2)25-21-17-13-11-9-7-5-6-8-10-12-14-20-24-28-40(49)60-36(31-57-39(48)27-23-19-16-15-18-22-26-35(3)4)32-58-63(53,54)62-64(55,56)59-33-37-41(50)42(51)43(61-37)47-30-29-38(45)46-44(47)52/h29-30,34-37,41-43,50-51H,5-28,31-33H2,1-4H3,(H,53,54)(H,55,56)(H2,45,46,52)/t36-,37-,41+,42?,43-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Isododecanoyl-2-isoeicosanoyl-sn-glycero-3-CDPHMDB
1-Isododecanoyl-2-isoeicosanoyl-sn-glycero-3-cytidine-5'-diphosphateHMDB
CDP-DG(32:0)HMDB
CDP-Diacylglycerol(I-12:0/I-20:0)HMDB
CDP-Diacylglycerol(32:0)HMDB
{[(2R,3R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-2-[(18-methylnonadecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinateHMDB
CDP-DG(i-12:0/i-20:0)SMPDB
Chemical FormulaC44H81N3O15P2
Average Molecular Weight954.086
Monoisotopic Molecular Weight953.514292916
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-2-[(18-methylnonadecanoyl)oxy]-3-[(10-methylundecanoyl)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)-2-[(18-methylnonadecanoyl)oxy]-3-[(10-methylundecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCC(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)CCCCCCCCCCCCCCCCC(C)C
InChI Identifier
InChI=1S/C44H81N3O15P2/c1-34(2)25-21-17-13-11-9-7-5-6-8-10-12-14-20-24-28-40(49)60-36(31-57-39(48)27-23-19-16-15-18-22-26-35(3)4)32-58-63(53,54)62-64(55,56)59-33-37-41(50)42(51)43(61-37)47-30-29-38(45)46-44(47)52/h29-30,34-37,41-43,50-51H,5-28,31-33H2,1-4H3,(H,53,54)(H,55,56)(H2,45,46,52)/t36-,37-,41+,42?,43-/m1/s1
InChI KeyBGBQRMYUYXUIPR-QDFYKRCGSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cdp-diacylglycerols. These are glycerolipids containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassCDP-glycerols
Direct ParentCDP-diacylglycerols
Alternative Parents
Substituents
  • Cdp-diacylglycerol
  • Pyrimidine ribonucleoside diphosphate
  • Diacyl-glycerol-3-pyrophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Fatty acid ester
  • Monoalkyl phosphate
  • Hydroxypyrimidine
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Alkyl phosphate
  • Hydropyrimidine
  • Pyrimidine
  • Phosphoric acid ester
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Carboxylic acid ester
  • 1,2-diol
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Carboxylic acid derivative
  • Organopnictogen compound
  • Organic oxide
  • Alcohol
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP5.7ALOGPS
logP9.24ChemAxon
logS-5.1ALOGPS
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 Count40ChemAxon
Refractivity240.11 m³·mol⁻¹ChemAxon
Polarizability105.4 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]+272.04830932474
DeepCCS[M-H]-270.22330932474
DeepCCS[M-2H]-303.66330932474
DeepCCS[M+Na]+277.65430932474
AllCCS[M+H]+299.832859911
AllCCS[M+H-H2O]+300.132859911
AllCCS[M+NH4]+299.532859911
AllCCS[M+Na]+299.432859911
AllCCS[M-H]-296.832859911
AllCCS[M+Na-2H]-303.632859911
AllCCS[M+HCOO]-311.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.10.46 minutes32390414
Predicted by Siyang on May 30, 202221.6144 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.95 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4216.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid138.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid315.6 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid174.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid782.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1271.5 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid1252.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)233.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2144.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1075.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2224.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid840.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid620.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate120.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA167.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water10.2 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - CDP-DG(i-12:0/i-20:0) 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-12:0/i-20:0) 10V, Positive-QTOFsplash10-03di-0910000001-dfe77a622e59e677010c2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 20V, Positive-QTOFsplash10-03di-1910000000-48e40f5becdeeb16a7012019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 40V, Positive-QTOFsplash10-03di-3920010000-28f6fda29b8a648a59052019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 10V, Negative-QTOFsplash10-0bu1-0901001002-61a42008cc737a09e43c2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 20V, Negative-QTOFsplash10-08gj-3901100100-a8a6f139496e640d4e1a2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 40V, Negative-QTOFsplash10-0bvi-4901000000-75142ac30147d0ca3ee82019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 10V, Negative-QTOFsplash10-0udi-0000000009-19c807ae5cbc2f7254912021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 20V, Negative-QTOFsplash10-002f-9222404002-ee66e52bb7c49ef971f52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 40V, Negative-QTOFsplash10-05qc-5549310202-f3bcfb07e0d6d14089ea2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 10V, Positive-QTOFsplash10-0udi-1100010029-5a29bc86c1575c0327b72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 20V, Positive-QTOFsplash10-03dj-2110010195-cbc5b01f997b5ea6a1b62021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-12:0/i-20:0) 40V, Positive-QTOFsplash10-0uka-0126900100-9d45188cdc21b26efe652021-09-22Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID74877878
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131822821
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