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Showing metabocard for CDP-DG(a-13:0/i-16:0) (HMDB0116072)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 06:54:22 UTC
Update Date2022-11-30 19:26:27 UTC
HMDB IDHMDB0116072
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(a-13:0/i-16:0)
DescriptionCDP-DG(a-13:0/i-16:0) 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(a-13:0/i-16:0), in particular, consists of one chain of anteisotridecanoic acid at the C-1 position and one chain of isohexadecanoic 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?1563873670
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116072 (CDP-DG(a-13:0/i-16:0))

CDP-DG(a-13:0/i-16:0)
  Mrv1652309161722262D          

 62 63  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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   14.5612   -4.5706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7337   -5.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3206   -5.7230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.4768   -4.2072    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
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   23.1992   -4.5116    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0116072 (CDP-DG(a-13:0/i-16:0))

HMDB0116072
     RDKit          3D
CDP-DG(a-13:0/i-16:0)
136137  0  0  0  0  0  0  0  0999 V2000
   -7.1128    5.8333   -1.8189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8679    4.4036   -2.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9466    3.6921   -1.3196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7518    3.7556    0.0425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7574    2.2555   -1.5413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2614    1.6929   -2.7892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9550    2.0276   -3.3740 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8336    3.4476   -3.7885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5273    3.7717   -4.4507 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.1869    4.1723   -1.8259 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3314    2.7892   -1.3768 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    2.0973   -1.1142 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.1204    1.2430   -0.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1710    2.5765   -0.4553 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3398    3.3153    0.4997 P   0  0  0  0  0  5  0  0  0  0  0  0
    6.1568    2.2662    1.2592 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.0358    6.5176   -2.6978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5186    4.4029   -3.3245 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8673    3.9204   -2.2988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0963    4.3205   -1.0911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6146    3.0590   -0.0487 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.9480    4.2066   -1.6883 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.4936   -5.3714   -4.6710 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.8494   -5.0344    2.5851 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116072 (CDP-DG(a-13:0/i-16:0))

CDP-DG(a-13:0/i-16:0)
  Mrv1652309161722262D          

 62 63  0  0  1  0            999 V2000
   17.4451   -4.0157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4838   -4.5706    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.5226   -4.0157    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4061   -4.5706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5612   -4.5706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7337   -5.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3206   -5.7230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.4768   -4.2072    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   19.4768   -5.3368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.8027   -4.5411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.4768   -3.1857    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.8732   -4.1777    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   21.8732   -5.3072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.1992   -4.5116    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.8732   -3.1563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.1589   -6.7486    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   26.0550   -5.2081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.1058   -5.8608    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   26.8357   -7.5484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.1528   -7.5601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.1017   -5.0357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.4120   -3.3822    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   28.4120   -4.2072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.6975   -2.9697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.6975   -4.6197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   26.9830   -3.3822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9830   -4.2072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.6976   -2.1447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   29.1119   -4.5018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8468   -4.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8468   -3.3867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.1327   -4.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4185   -4.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7044   -4.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9903   -4.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2762   -4.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5620   -4.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8479   -4.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1337   -4.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4196   -4.5712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7054   -4.1581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7054   -4.9831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9913   -4.5700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0193   -6.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0193   -6.8646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   13.5910   -6.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8769   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1627   -6.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4486   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0213   -5.2681    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  2  6  1  0  0  0  0
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 12 10  1  0  0  0  0
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 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
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 18 27  1  1  0  0  0
 19 20  1  0  0  0  0
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 24 25  1  0  0  0  0
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 32  5  1  0  0  0  0
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 37 38  1  0  0  0  0
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 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
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 42 44  1  0  0  0  0
 44 45  1  0  0  0  0
 46  6  1  0  0  0  0
 46 47  2  0  0  0  0
 46 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  1  0  0  0  0
 51 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 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  1  0  0  0  0
 60 62  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0116072

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C41H75N3O15P2/c1-5-32(4)23-19-15-12-13-16-20-24-36(45)54-28-33(57-37(46)25-21-17-11-9-7-6-8-10-14-18-22-31(2)3)29-55-60(50,51)59-61(52,53)56-30-34-38(47)39(48)40(58-34)44-27-26-35(42)43-41(44)49/h26-27,31-34,38-40,47-48H,5-25,28-30H2,1-4H3,(H,50,51)(H,52,53)(H2,42,43,49)/t32?,33-,34-,38+,39?,40-/m1/s1

> <INCHI_KEY>
VJGSENPAPFROFZ-WERIVYNPSA-N

> <FORMULA>
C41H75N3O15P2

> <MOLECULAR_WEIGHT>
912.005

> <EXACT_MASS>
911.467342723

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
136

> <JCHEM_AVERAGE_POLARIZABILITY>
97.60329010542739

> <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-[(10-methyldodecanoyl)oxy]-2-[(14-methylpentadecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
5.02

> <JCHEM_LOGP>
7.907944646333334

> <ALOGPS_LOGS>
-4.75

> <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>
226.30270000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
37

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.62e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-[(10-methyldodecanoyl)oxy]-2-[(14-methylpentadecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116072 (CDP-DG(a-13:0/i-16:0))

HMDB0116072
     RDKit          3D
CDP-DG(a-13:0/i-16:0)
136137  0  0  0  0  0  0  0  0999 V2000
   -7.1128    5.8333   -1.8189 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8679    4.4036   -2.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9466    3.6921   -1.3196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7518    3.7556    0.0425 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7574    2.2555   -1.5413 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0116072 (CDP-DG(a-13:0/i-16:0))

HEADER    PROTEIN                                 16-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(a-13:0/i-16:0)                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-SEP-17         0                                  
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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      11.184  -8.531   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      28.036 -11.374   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0      28.036 -12.814   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0      26.703 -10.603   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      25.370 -11.374   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      24.037 -10.603   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      22.704 -11.374   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      21.371 -10.603   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      20.038 -11.374   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      18.705 -10.603   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      17.372 -11.374   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      16.038 -10.603   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      14.705 -11.374   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      13.372 -10.603   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      12.039 -11.374   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      10.706 -10.603   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       9.373 -11.374   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       9.373  -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   46                                                       
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   45                                                       
CONECT   45   44                                                            
CONECT   46    6   47   48                                                  
CONECT   47   46                                                            
CONECT   48   46   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   62                                                  
CONECT   61   60                                                            
CONECT   62   60                                                            
MASTER        0    0    0    0    0    0    0    0   62    0  126    0
END
Download

3D PDB for HMDB0116072 (CDP-DG(a-13:0/i-16:0))

COMPND    HMDB0116072
HETATM    1  C1  UNL     1      -7.113   5.833  -1.819  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.868   4.404  -2.273  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.947   3.692  -1.320  1.00  0.00           C  
HETATM    4  C4  UNL     1      -6.752   3.756   0.042  1.00  0.00           C  
HETATM    5  C5  UNL     1      -5.757   2.255  -1.541  1.00  0.00           C  
HETATM    6  C6  UNL     1      -5.261   1.693  -2.789  1.00  0.00           C  
HETATM    7  C7  UNL     1      -3.955   2.028  -3.374  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.834   3.448  -3.789  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.527   3.772  -4.451  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.292   3.597  -3.685  1.00  0.00           C  
HETATM   11  C11 UNL     1      -1.181   4.482  -2.437  1.00  0.00           C  
HETATM   12  C12 UNL     1       0.187   4.172  -1.826  1.00  0.00           C  
HETATM   13  C13 UNL     1       0.331   2.789  -1.377  1.00  0.00           C  
HETATM   14  O1  UNL     1      -0.683   2.097  -1.114  1.00  0.00           O  
HETATM   15  O2  UNL     1       1.556   2.157  -1.214  1.00  0.00           O  
HETATM   16  C14 UNL     1       1.723   0.833  -0.770  1.00  0.00           C  
HETATM   17  C15 UNL     1       3.175   0.400  -0.874  1.00  0.00           C  
HETATM   18  C16 UNL     1       4.120   1.243  -0.092  1.00  0.00           C  
HETATM   19  O3  UNL     1       4.171   2.576  -0.455  1.00  0.00           O  
HETATM   20  P1  UNL     1       5.340   3.315   0.500  1.00  0.00           P  
HETATM   21  O4  UNL     1       6.157   2.266   1.259  1.00  0.00           O  
HETATM   22  O5  UNL     1       6.471   4.155  -0.451  1.00  0.00           O  
HETATM   23  O6  UNL     1       4.750   4.386   1.631  1.00  0.00           O  
HETATM   24  P2  UNL     1       3.148   4.767   1.388  1.00  0.00           P  
HETATM   25  O7  UNL     1       2.891   4.965  -0.083  1.00  0.00           O  
HETATM   26  O8  UNL     1       2.731   6.235   2.165  1.00  0.00           O  
HETATM   27  O9  UNL     1       2.145   3.589   2.069  1.00  0.00           O  
HETATM   28  C17 UNL     1       2.753   3.036   3.220  1.00  0.00           C  
HETATM   29  C18 UNL     1       1.810   2.010   3.754  1.00  0.00           C  
HETATM   30  O10 UNL     1       2.322   1.375   4.912  1.00  0.00           O  
HETATM   31  C19 UNL     1       1.227   0.522   5.189  1.00  0.00           C  
HETATM   32  N1  UNL     1       1.464  -0.304   6.324  1.00  0.00           N  
HETATM   33  C20 UNL     1       1.094  -1.602   6.300  1.00  0.00           C  
HETATM   34  C21 UNL     1       1.309  -2.447   7.381  1.00  0.00           C  
HETATM   35  C22 UNL     1       1.921  -1.956   8.530  1.00  0.00           C  
HETATM   36  N2  UNL     1       2.160  -2.794   9.651  1.00  0.00           N  
HETATM   37  N3  UNL     1       2.271  -0.659   8.509  1.00  0.00           N  
HETATM   38  C23 UNL     1       2.053   0.140   7.448  1.00  0.00           C  
HETATM   39  O11 UNL     1       2.392   1.367   7.446  1.00  0.00           O  
HETATM   40  C24 UNL     1       0.129   1.527   5.320  1.00  0.00           C  
HETATM   41  O12 UNL     1      -1.082   0.926   4.975  1.00  0.00           O  
HETATM   42  C25 UNL     1       0.524   2.569   4.269  1.00  0.00           C  
HETATM   43  O13 UNL     1       0.794   3.750   4.928  1.00  0.00           O  
HETATM   44  O14 UNL     1       3.585   0.437  -2.237  1.00  0.00           O  
HETATM   45  C26 UNL     1       4.030  -0.730  -2.842  1.00  0.00           C  
HETATM   46  O15 UNL     1       4.092  -1.796  -2.213  1.00  0.00           O  
HETATM   47  C27 UNL     1       4.429  -0.672  -4.257  1.00  0.00           C  
HETATM   48  C28 UNL     1       4.963  -1.927  -4.829  1.00  0.00           C  
HETATM   49  C29 UNL     1       4.012  -3.106  -4.801  1.00  0.00           C  
HETATM   50  C30 UNL     1       2.753  -2.862  -5.546  1.00  0.00           C  
HETATM   51  C31 UNL     1       1.790  -3.988  -5.576  1.00  0.00           C  
HETATM   52  C32 UNL     1       1.075  -4.423  -4.369  1.00  0.00           C  
HETATM   53  C33 UNL     1       1.870  -4.811  -3.191  1.00  0.00           C  
HETATM   54  C34 UNL     1       0.965  -5.390  -2.079  1.00  0.00           C  
HETATM   55  C35 UNL     1       1.883  -5.733  -0.927  1.00  0.00           C  
HETATM   56  C36 UNL     1       1.166  -6.343   0.237  1.00  0.00           C  
HETATM   57  C37 UNL     1       0.098  -5.461   0.822  1.00  0.00           C  
HETATM   58  C38 UNL     1       0.598  -4.146   1.334  1.00  0.00           C  
HETATM   59  C39 UNL     1      -0.603  -3.394   1.884  1.00  0.00           C  
HETATM   60  C40 UNL     1      -0.185  -2.057   2.419  1.00  0.00           C  
HETATM   61  C41 UNL     1      -1.282  -4.173   2.984  1.00  0.00           C  
HETATM   62  H1  UNL     1      -8.097   5.960  -1.366  1.00  0.00           H  
HETATM   63  H2  UNL     1      -6.339   6.195  -1.109  1.00  0.00           H  
HETATM   64  H3  UNL     1      -7.036   6.518  -2.698  1.00  0.00           H  
HETATM   65  H4  UNL     1      -6.519   4.403  -3.325  1.00  0.00           H  
HETATM   66  H5  UNL     1      -7.867   3.920  -2.299  1.00  0.00           H  
HETATM   67  H6  UNL     1      -5.096   4.320  -1.091  1.00  0.00           H  
HETATM   68  H7  UNL     1      -7.615   3.059  -0.049  1.00  0.00           H  
HETATM   69  H8  UNL     1      -7.096   4.786   0.101  1.00  0.00           H  
HETATM   70  H9  UNL     1      -6.025   3.510   0.811  1.00  0.00           H  
HETATM   71  H10 UNL     1      -5.165   1.862  -0.661  1.00  0.00           H  
HETATM   72  H11 UNL     1      -6.784   1.771  -1.325  1.00  0.00           H  
HETATM   73  H12 UNL     1      -5.304   0.543  -2.654  1.00  0.00           H  
HETATM   74  H13 UNL     1      -6.033   1.800  -3.630  1.00  0.00           H  
HETATM   75  H14 UNL     1      -3.848   1.392  -4.317  1.00  0.00           H  
HETATM   76  H15 UNL     1      -3.084   1.675  -2.764  1.00  0.00           H  
HETATM   77  H16 UNL     1      -4.618   3.663  -4.578  1.00  0.00           H  
HETATM   78  H17 UNL     1      -4.026   4.200  -3.015  1.00  0.00           H  
HETATM   79  H18 UNL     1      -2.541   3.257  -5.438  1.00  0.00           H  
HETATM   80  H19 UNL     1      -2.601   4.868  -4.726  1.00  0.00           H  
HETATM   81  H20 UNL     1      -1.076   2.564  -3.348  1.00  0.00           H  
HETATM   82  H21 UNL     1      -0.418   3.876  -4.347  1.00  0.00           H  
HETATM   83  H22 UNL     1      -1.269   5.543  -2.656  1.00  0.00           H  
HETATM   84  H23 UNL     1      -1.948   4.207  -1.688  1.00  0.00           H  
HETATM   85  H24 UNL     1       0.311   4.880  -0.962  1.00  0.00           H  
HETATM   86  H25 UNL     1       0.943   4.483  -2.583  1.00  0.00           H  
HETATM   87  H26 UNL     1       1.077   0.144  -1.335  1.00  0.00           H  
HETATM   88  H27 UNL     1       1.426   0.783   0.291  1.00  0.00           H  
HETATM   89  H28 UNL     1       3.253  -0.633  -0.511  1.00  0.00           H  
HETATM   90  H29 UNL     1       5.175   0.863  -0.226  1.00  0.00           H  
HETATM   91  H30 UNL     1       3.948   1.206   1.006  1.00  0.00           H  
HETATM   92  H31 UNL     1       7.183   3.569  -0.781  1.00  0.00           H  
HETATM   93  H32 UNL     1       3.090   6.259   3.091  1.00  0.00           H  
HETATM   94  H33 UNL     1       2.852   3.903   3.924  1.00  0.00           H  
HETATM   95  H34 UNL     1       3.710   2.602   2.942  1.00  0.00           H  
HETATM   96  H35 UNL     1       1.694   1.204   3.001  1.00  0.00           H  
HETATM   97  H36 UNL     1       1.085  -0.105   4.292  1.00  0.00           H  
HETATM   98  H37 UNL     1       0.614  -1.969   5.393  1.00  0.00           H  
HETATM   99  H38 UNL     1       1.016  -3.487   7.368  1.00  0.00           H  
HETATM  100  H39 UNL     1       2.940  -3.478   9.592  1.00  0.00           H  
HETATM  101  H40 UNL     1       1.606  -2.770  10.529  1.00  0.00           H  
HETATM  102  H41 UNL     1       0.096   1.977   6.330  1.00  0.00           H  
HETATM  103  H42 UNL     1      -1.402   1.381   4.145  1.00  0.00           H  
HETATM  104  H43 UNL     1      -0.269   2.685   3.505  1.00  0.00           H  
HETATM  105  H44 UNL     1       1.123   3.590   5.843  1.00  0.00           H  
HETATM  106  H45 UNL     1       3.505  -0.326  -4.811  1.00  0.00           H  
HETATM  107  H46 UNL     1       5.156   0.156  -4.428  1.00  0.00           H  
HETATM  108  H47 UNL     1       5.378  -1.795  -5.864  1.00  0.00           H  
HETATM  109  H48 UNL     1       5.851  -2.234  -4.212  1.00  0.00           H  
HETATM  110  H49 UNL     1       3.940  -3.433  -3.780  1.00  0.00           H  
HETATM  111  H50 UNL     1       4.592  -3.934  -5.335  1.00  0.00           H  
HETATM  112  H51 UNL     1       3.050  -2.609  -6.614  1.00  0.00           H  
HETATM  113  H52 UNL     1       2.233  -1.926  -5.199  1.00  0.00           H  
HETATM  114  H53 UNL     1       2.358  -4.905  -6.019  1.00  0.00           H  
HETATM  115  H54 UNL     1       1.055  -3.815  -6.447  1.00  0.00           H  
HETATM  116  H55 UNL     1       0.229  -3.719  -4.092  1.00  0.00           H  
HETATM  117  H56 UNL     1       0.494  -5.371  -4.671  1.00  0.00           H  
HETATM  118  H57 UNL     1       2.188  -3.830  -2.685  1.00  0.00           H  
HETATM  119  H58 UNL     1       2.721  -5.441  -3.315  1.00  0.00           H  
HETATM  120  H59 UNL     1       0.457  -6.303  -2.399  1.00  0.00           H  
HETATM  121  H60 UNL     1       0.269  -4.605  -1.724  1.00  0.00           H  
HETATM  122  H61 UNL     1       2.677  -6.460  -1.227  1.00  0.00           H  
HETATM  123  H62 UNL     1       2.427  -4.834  -0.567  1.00  0.00           H  
HETATM  124  H63 UNL     1       0.791  -7.358   0.013  1.00  0.00           H  
HETATM  125  H64 UNL     1       1.938  -6.479   1.046  1.00  0.00           H  
HETATM  126  H65 UNL     1      -0.695  -5.323   0.051  1.00  0.00           H  
HETATM  127  H66 UNL     1      -0.303  -6.020   1.712  1.00  0.00           H  
HETATM  128  H67 UNL     1       1.337  -4.284   2.127  1.00  0.00           H  
HETATM  129  H68 UNL     1       1.037  -3.551   0.496  1.00  0.00           H  
HETATM  130  H69 UNL     1      -1.366  -3.245   1.079  1.00  0.00           H  
HETATM  131  H70 UNL     1       0.871  -2.047   2.724  1.00  0.00           H  
HETATM  132  H71 UNL     1      -0.784  -1.807   3.334  1.00  0.00           H  
HETATM  133  H72 UNL     1      -0.376  -1.237   1.687  1.00  0.00           H  
HETATM  134  H73 UNL     1      -2.003  -3.483   3.498  1.00  0.00           H  
HETATM  135  H74 UNL     1      -0.580  -4.528   3.760  1.00  0.00           H  
HETATM  136  H75 UNL     1      -1.849  -5.034   2.585  1.00  0.00           H  
CONECT    1    2   62   63   64
CONECT    2    3   65   66
CONECT    3    4    5   67
CONECT    4   68   69   70
CONECT    5    6   71   72
CONECT    6    7   73   74
CONECT    7    8   75   76
CONECT    8    9   77   78
CONECT    9   10   79   80
CONECT   10   11   81   82
CONECT   11   12   83   84
CONECT   12   13   85   86
CONECT   13   14   14   15
CONECT   15   16
CONECT   16   17   87   88
CONECT   17   18   44   89
CONECT   18   19   90   91
CONECT   19   20
CONECT   20   21   21   22   23
CONECT   22   92
CONECT   23   24
CONECT   24   25   25   26   27
CONECT   26   93
CONECT   27   28
CONECT   28   29   94   95
CONECT   29   30   42   96
CONECT   30   31
CONECT   31   32   40   97
CONECT   32   33   38
CONECT   33   34   34   98
CONECT   34   35   99
CONECT   35   36   37   37
CONECT   36  100  101
CONECT   37   38
CONECT   38   39   39
CONECT   40   41   42  102
CONECT   41  103
CONECT   42   43  104
CONECT   43  105
CONECT   44   45
CONECT   45   46   46   47
CONECT   47   48  106  107
CONECT   48   49  108  109
CONECT   49   50  110  111
CONECT   50   51  112  113
CONECT   51   52  114  115
CONECT   52   53  116  117
CONECT   53   54  118  119
CONECT   54   55  120  121
CONECT   55   56  122  123
CONECT   56   57  124  125
CONECT   57   58  126  127
CONECT   58   59  128  129
CONECT   59   60   61  130
CONECT   60  131  132  133
CONECT   61  134  135  136
END
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SMILES for HMDB0116072 (CDP-DG(a-13:0/i-16:0))

[H][C@@](COC(=O)CCCCCCCCC(C)CC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCC(C)C
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INCHI for HMDB0116072 (CDP-DG(a-13:0/i-16:0))

InChI=1S/C41H75N3O15P2/c1-5-32(4)23-19-15-12-13-16-20-24-36(45)54-28-33(57-37(46)25-21-17-11-9-7-6-8-10-14-18-22-31(2)3)29-55-60(50,51)59-61(52,53)56-30-34-38(47)39(48)40(58-34)44-27-26-35(42)43-41(44)49/h26-27,31-34,38-40,47-48H,5-25,28-30H2,1-4H3,(H,50,51)(H,52,53)(H2,42,43,49)/t32?,33-,34-,38+,39?,40-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-anteisotridecanoyl-2-isohexadecanoyl-sn-glycero-3-CDPSMPDB, HMDB
1-anteisotridecanoyl-2-isohexadecanoyl-sn-glycero-3-cytidine-5'-diphosphateSMPDB, HMDB
CDP-DG(a-13:0/i-16:0)SMPDB
CDP-DG(29:0)SMPDB, HMDB
CDP-diacylglycerol(a-13:0/i-16:0)SMPDB, HMDB
CDP-diacylglycerol(29:0)SMPDB, HMDB
{[(2R,3R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(10-methyldodecanoyl)oxy]-2-[(14-methylpentadecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinateGenerator, HMDB
Chemical FormulaC41H75N3O15P2
Average Molecular Weight912.005
Monoisotopic Molecular Weight911.467342723
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(10-methyldodecanoyl)oxy]-2-[(14-methylpentadecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-[(10-methyldodecanoyl)oxy]-2-[(14-methylpentadecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCC(C)CC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCC(C)C
InChI Identifier
InChI=1S/C41H75N3O15P2/c1-5-32(4)23-19-15-12-13-16-20-24-36(45)54-28-33(57-37(46)25-21-17-11-9-7-6-8-10-14-18-22-31(2)3)29-55-60(50,51)59-61(52,53)56-30-34-38(47)39(48)40(58-34)44-27-26-35(42)43-41(44)49/h26-27,31-34,38-40,47-48H,5-25,28-30H2,1-4H3,(H,50,51)(H,52,53)(H2,42,43,49)/t32?,33-,34-,38+,39?,40-/m1/s1
InChI KeyVJGSENPAPFROFZ-WERIVYNPSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cdp-diacylglycerols. These are glycerolipids containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassCDP-glycerols
Direct ParentCDP-diacylglycerols
Alternative Parents
Substituents
  • Cdp-diacylglycerol
  • Pyrimidine ribonucleoside diphosphate
  • Diacyl-glycerol-3-pyrophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Fatty acid ester
  • Monoalkyl phosphate
  • Hydroxypyrimidine
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Alkyl phosphate
  • Hydropyrimidine
  • Pyrimidine
  • Phosphoric acid ester
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Carboxylic acid ester
  • 1,2-diol
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Carboxylic acid derivative
  • Organopnictogen compound
  • Organic oxide
  • Alcohol
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
DispositionNot Available
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP5.02ALOGPS
logP7.91ChemAxon
logS-4.8ALOGPS
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 Count37ChemAxon
Refractivity226.3 m³·mol⁻¹ChemAxon
Polarizability97.6 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]+266.69330932474
DeepCCS[M-H]-264.86830932474
DeepCCS[M-2H]-298.61530932474
DeepCCS[M+Na]+272.39130932474
AllCCS[M+H]+291.432859911
AllCCS[M+H-H2O]+291.832859911
AllCCS[M+NH4]+291.132859911
AllCCS[M+Na]+291.032859911
AllCCS[M-H]-287.232859911
AllCCS[M+Na-2H]-293.632859911
AllCCS[M+HCOO]-300.632859911

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - CDP-DG(a-13:0/i-16:0) 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(a-13:0/i-16:0) 10V, Positive-QTOFsplash10-03di-0910001000-14a47c2c0351513481952019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 20V, Positive-QTOFsplash10-03di-1910000000-9fad6f031f6ec82aad6a2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 40V, Positive-QTOFsplash10-03di-3920000000-bfa9d72b1bed5830ce492019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 10V, Negative-QTOFsplash10-08fr-0950002011-8b6a62389ea5a592ff162019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 20V, Negative-QTOFsplash10-03di-4952202010-96cf24147241534f55bd2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 40V, Negative-QTOFsplash10-0bvi-5921000000-342c2c950cd180412e1e2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 10V, Positive-QTOFsplash10-03di-5000010197-2e5e94db00230d18ecd12021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 20V, Positive-QTOFsplash10-0a4i-9100000480-8cacd7b5fd35090058e92021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 40V, Positive-QTOFsplash10-006w-0029100000-e6b1763178867d9b39e52021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 10V, Negative-QTOFsplash10-03di-0000000019-9c199d1530ca5371c7ed2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 20V, Negative-QTOFsplash10-06vl-9140514011-c047d07f7e2770d680742021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-16:0) 40V, Negative-QTOFsplash10-05rr-5439504020-f6ff08ff8031ca78839e2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131822728
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