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Showing metabocard for CDP-DG(a-13:0/i-12:0) (HMDB0116068)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 06:53:28 UTC
Update Date2022-11-30 19:26:27 UTC
HMDB IDHMDB0116068
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(a-13:0/i-12:0)
DescriptionCDP-DG(a-13:0/i-12:0) 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-12:0), in particular, consists of one chain of anteisotridecanoic acid at the C-1 position and one chain of isododecanoic 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?1563873669
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116068 (CDP-DG(a-13:0/i-12:0))

CDP-DG(a-13:0/i-12:0)
  Mrv1652309161722252D          

 58 59  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
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   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
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M  END
Download

3D MOL for HMDB0116068 (CDP-DG(a-13:0/i-12:0))

HMDB0116068
     RDKit          3D
CDP-DG(a-13:0/i-12:0)
124125  0  0  0  0  0  0  0  0999 V2000
   -5.0415    0.2561    1.8821 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4171   -0.6374    0.7343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5871   -1.8785    0.6524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1088   -1.5134    0.4600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7563   -2.7244    1.8788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1931   -3.1338    2.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4213   -3.9884    3.2530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6559   -5.2766    3.2155 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0436   -6.1145    2.0187 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.9971    7.1403   -1.1890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6589    4.6478   -4.6984 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3282    3.8103   -5.9375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0145    3.0120   -4.8785 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8628    2.1567   -6.5988 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8223   -5.1167   -0.2004 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6034   -3.5627   -1.0234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2583   -3.4356    0.8202 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9970   -3.9408    1.9591 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9080   -1.3584    0.2978 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7454   -1.9024    1.5283 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7120   -1.3681    2.0046 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4723   -1.9151    3.2629 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4818    0.6453    1.5824 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1993    0.2004    2.7620 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0257    0.1116    4.5707 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2135    0.6120    3.3342 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4334    2.4576    4.7472 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7440    2.1652    4.2258 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3058    2.6333    1.8906 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0323    2.9115    2.3012 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5995    4.4374    3.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5706    5.9969    4.2363 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6214    4.5626    3.9321 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.8112    5.7899    1.7482 H   0  0  0  0  0  0  0  0  0  0  0  0
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 57124  1  0
M  END
Download

3D SDF for HMDB0116068 (CDP-DG(a-13:0/i-12:0))

CDP-DG(a-13:0/i-12:0)
  Mrv1652309161722252D          

 58 59  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
   26.8306   -6.7486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.7371   -5.8702    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   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
   14.3052   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   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
   10.7344   -6.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0203   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3062   -6.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5920   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8779   -6.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8779   -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
  2  7  1  1  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  8  4  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  2  0  0  0  0
 12 10  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 12 15  2  0  0  0  0
 14 23  1  0  0  0  0
 16 17  1  0  0  0  0
 16 22  1  1  0  0  0
 18 19  1  0  0  0  0
 18 17  1  0  0  0  0
 18 27  1  1  0  0  0
 19 20  1  0  0  0  0
 20 16  1  0  0  0  0
 20 23  1  1  0  0  0
 21 17  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
 25 27  1  0  0  0  0
 25 31  2  0  0  0  0
 26 28  1  0  0  0  0
 26 30  1  0  0  0  0
 27 29  1  0  0  0  0
 28 29  2  0  0  0  0
 32  5  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 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
 56 58  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0116068

> <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)CCCCCCCCC(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C37H67N3O15P2/c1-5-28(4)19-15-11-7-9-12-16-20-32(41)50-24-29(53-33(42)21-17-13-8-6-10-14-18-27(2)3)25-51-56(46,47)55-57(48,49)52-26-30-34(43)35(44)36(54-30)40-23-22-31(38)39-37(40)45/h22-23,27-30,34-36,43-44H,5-21,24-26H2,1-4H3,(H,46,47)(H,48,49)(H2,38,39,45)/t28?,29-,30-,34+,35?,36-/m1/s1

> <INCHI_KEY>
URXLTEPIZQRTAV-WXBMFJRSSA-N

> <FORMULA>
C37H67N3O15P2

> <MOLECULAR_WEIGHT>
855.897

> <EXACT_MASS>
855.404742465

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
124

> <JCHEM_AVERAGE_POLARIZABILITY>
89.07296146865886

> <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-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
3.79

> <JCHEM_LOGP>
6.129669986333333

> <ALOGPS_LOGS>
-4.09

> <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>
207.89870000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
33

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.95e-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-[(10-methylundecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116068 (CDP-DG(a-13:0/i-12:0))

HMDB0116068
     RDKit          3D
CDP-DG(a-13:0/i-12:0)
124125  0  0  0  0  0  0  0  0999 V2000
   -5.0415    0.2561    1.8821 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4171   -0.6374    0.7343 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5871   -1.8785    0.6524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1088   -1.5134    0.4600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7563   -2.7244    1.8788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1931   -3.1338    2.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4213   -3.9884    3.2530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6559   -5.2766    3.2155 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0436   -6.1145    2.0187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2797   -7.4223    2.0980 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6007   -8.3326    0.9549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2144   -7.7840   -0.4013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7686   -7.5810   -0.5244 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0324   -8.6214   -0.6277 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1172   -6.3659   -0.5393 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6804   -6.3244   -0.6656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2460   -4.9046   -0.6503 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9923   -4.1286   -1.7024 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6503   -4.5234   -2.9930 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5061   -3.6253   -4.1231 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.0017   -3.8982   -4.0614 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9753   -4.0752   -5.6792 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2738   -1.9786   -3.9698 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7088   -1.5092   -4.4102 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.5156   -1.8521   -5.8624 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3695   -2.3654   -3.4217 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4544    0.1265   -4.2008 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7929    0.3155   -3.6105 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9872    1.7942   -3.4382 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2356    2.0866   -2.8394 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0116068 (CDP-DG(a-13:0/i-12:0))

HEADER    PROTEIN                                 16-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(a-13:0/i-12:0)                             
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      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      14.705  -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   58                                                  
CONECT   57   56                                                            
CONECT   58   56                                                            
MASTER        0    0    0    0    0    0    0    0   58    0  118    0
END
Download

3D PDB for HMDB0116068 (CDP-DG(a-13:0/i-12:0))

COMPND    HMDB0116068
HETATM    1  C1  UNL     1      -5.041   0.256   1.882  1.00  0.00           C  
HETATM    2  C2  UNL     1      -5.417  -0.637   0.734  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.587  -1.879   0.652  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.109  -1.513   0.460  1.00  0.00           C  
HETATM    5  C5  UNL     1      -4.756  -2.724   1.879  1.00  0.00           C  
HETATM    6  C6  UNL     1      -6.193  -3.134   2.043  1.00  0.00           C  
HETATM    7  C7  UNL     1      -6.421  -3.988   3.253  1.00  0.00           C  
HETATM    8  C8  UNL     1      -5.656  -5.277   3.216  1.00  0.00           C  
HETATM    9  C9  UNL     1      -6.044  -6.114   2.019  1.00  0.00           C  
HETATM   10  C10 UNL     1      -5.280  -7.422   2.098  1.00  0.00           C  
HETATM   11  C11 UNL     1      -5.601  -8.333   0.955  1.00  0.00           C  
HETATM   12  C12 UNL     1      -5.214  -7.784  -0.401  1.00  0.00           C  
HETATM   13  C13 UNL     1      -3.769  -7.581  -0.524  1.00  0.00           C  
HETATM   14  O1  UNL     1      -3.032  -8.621  -0.628  1.00  0.00           O  
HETATM   15  O2  UNL     1      -3.117  -6.366  -0.539  1.00  0.00           O  
HETATM   16  C14 UNL     1      -1.680  -6.324  -0.666  1.00  0.00           C  
HETATM   17  C15 UNL     1      -1.246  -4.905  -0.650  1.00  0.00           C  
HETATM   18  C16 UNL     1      -1.992  -4.129  -1.702  1.00  0.00           C  
HETATM   19  O3  UNL     1      -1.650  -4.523  -2.993  1.00  0.00           O  
HETATM   20  P1  UNL     1      -2.506  -3.625  -4.123  1.00  0.00           P  
HETATM   21  O4  UNL     1      -4.002  -3.898  -4.061  1.00  0.00           O  
HETATM   22  O5  UNL     1      -1.975  -4.075  -5.679  1.00  0.00           O  
HETATM   23  O6  UNL     1      -2.274  -1.979  -3.970  1.00  0.00           O  
HETATM   24  P2  UNL     1      -0.709  -1.509  -4.410  1.00  0.00           P  
HETATM   25  O7  UNL     1      -0.516  -1.852  -5.862  1.00  0.00           O  
HETATM   26  O8  UNL     1       0.370  -2.365  -3.422  1.00  0.00           O  
HETATM   27  O9  UNL     1      -0.454   0.126  -4.201  1.00  0.00           O  
HETATM   28  C17 UNL     1       0.793   0.315  -3.611  1.00  0.00           C  
HETATM   29  C18 UNL     1       0.987   1.794  -3.438  1.00  0.00           C  
HETATM   30  O10 UNL     1       2.236   2.087  -2.839  1.00  0.00           O  
HETATM   31  C19 UNL     1       2.218   3.477  -2.941  1.00  0.00           C  
HETATM   32  N1  UNL     1       3.363   4.123  -2.391  1.00  0.00           N  
HETATM   33  C20 UNL     1       4.519   3.515  -2.095  1.00  0.00           C  
HETATM   34  C21 UNL     1       5.573   4.238  -1.560  1.00  0.00           C  
HETATM   35  C22 UNL     1       5.470   5.596  -1.316  1.00  0.00           C  
HETATM   36  N2  UNL     1       6.568   6.310  -0.767  1.00  0.00           N  
HETATM   37  N3  UNL     1       4.294   6.170  -1.626  1.00  0.00           N  
HETATM   38  C23 UNL     1       3.278   5.452  -2.146  1.00  0.00           C  
HETATM   39  O11 UNL     1       2.215   6.064  -2.407  1.00  0.00           O  
HETATM   40  C24 UNL     1       2.054   3.652  -4.435  1.00  0.00           C  
HETATM   41  O12 UNL     1       3.255   3.359  -5.044  1.00  0.00           O  
HETATM   42  C25 UNL     1       1.025   2.549  -4.726  1.00  0.00           C  
HETATM   43  O13 UNL     1       1.394   1.808  -5.825  1.00  0.00           O  
HETATM   44  O14 UNL     1       0.153  -4.751  -0.758  1.00  0.00           O  
HETATM   45  C26 UNL     1       0.937  -4.161   0.211  1.00  0.00           C  
HETATM   46  O15 UNL     1       0.375  -3.738   1.236  1.00  0.00           O  
HETATM   47  C27 UNL     1       2.390  -4.087  -0.062  1.00  0.00           C  
HETATM   48  C28 UNL     1       3.184  -3.398   1.007  1.00  0.00           C  
HETATM   49  C29 UNL     1       2.797  -1.973   1.229  1.00  0.00           C  
HETATM   50  C30 UNL     1       3.658  -1.364   2.324  1.00  0.00           C  
HETATM   51  C31 UNL     1       3.267   0.096   2.543  1.00  0.00           C  
HETATM   52  C32 UNL     1       4.135   0.670   3.626  1.00  0.00           C  
HETATM   53  C33 UNL     1       3.809   2.119   3.898  1.00  0.00           C  
HETATM   54  C34 UNL     1       4.005   2.983   2.678  1.00  0.00           C  
HETATM   55  C35 UNL     1       3.663   4.425   3.030  1.00  0.00           C  
HETATM   56  C36 UNL     1       4.580   4.882   4.140  1.00  0.00           C  
HETATM   57  C37 UNL     1       3.819   5.309   1.826  1.00  0.00           C  
HETATM   58  H1  UNL     1      -4.840   1.306   1.533  1.00  0.00           H  
HETATM   59  H2  UNL     1      -5.892   0.359   2.601  1.00  0.00           H  
HETATM   60  H3  UNL     1      -4.201  -0.139   2.470  1.00  0.00           H  
HETATM   61  H4  UNL     1      -6.477  -0.886   0.777  1.00  0.00           H  
HETATM   62  H5  UNL     1      -5.297  -0.049  -0.224  1.00  0.00           H  
HETATM   63  H6  UNL     1      -4.892  -2.427  -0.263  1.00  0.00           H  
HETATM   64  H7  UNL     1      -2.513  -2.360   0.812  1.00  0.00           H  
HETATM   65  H8  UNL     1      -2.980  -1.279  -0.597  1.00  0.00           H  
HETATM   66  H9  UNL     1      -2.822  -0.631   1.061  1.00  0.00           H  
HETATM   67  H10 UNL     1      -4.428  -2.136   2.762  1.00  0.00           H  
HETATM   68  H11 UNL     1      -4.125  -3.635   1.751  1.00  0.00           H  
HETATM   69  H12 UNL     1      -6.817  -2.214   2.157  1.00  0.00           H  
HETATM   70  H13 UNL     1      -6.560  -3.650   1.126  1.00  0.00           H  
HETATM   71  H14 UNL     1      -6.129  -3.453   4.196  1.00  0.00           H  
HETATM   72  H15 UNL     1      -7.496  -4.259   3.383  1.00  0.00           H  
HETATM   73  H16 UNL     1      -4.571  -5.019   3.195  1.00  0.00           H  
HETATM   74  H17 UNL     1      -5.811  -5.849   4.174  1.00  0.00           H  
HETATM   75  H18 UNL     1      -5.783  -5.536   1.118  1.00  0.00           H  
HETATM   76  H19 UNL     1      -7.122  -6.349   2.044  1.00  0.00           H  
HETATM   77  H20 UNL     1      -5.595  -7.929   3.026  1.00  0.00           H  
HETATM   78  H21 UNL     1      -4.192  -7.219   2.126  1.00  0.00           H  
HETATM   79  H22 UNL     1      -6.678  -8.568   0.927  1.00  0.00           H  
HETATM   80  H23 UNL     1      -5.015  -9.264   1.098  1.00  0.00           H  
HETATM   81  H24 UNL     1      -5.540  -8.573  -1.141  1.00  0.00           H  
HETATM   82  H25 UNL     1      -5.776  -6.874  -0.666  1.00  0.00           H  
HETATM   83  H26 UNL     1      -1.361  -6.888  -1.565  1.00  0.00           H  
HETATM   84  H27 UNL     1      -1.286  -6.878   0.213  1.00  0.00           H  
HETATM   85  H28 UNL     1      -1.525  -4.473   0.333  1.00  0.00           H  
HETATM   86  H29 UNL     1      -3.073  -4.231  -1.497  1.00  0.00           H  
HETATM   87  H30 UNL     1      -1.731  -3.063  -1.581  1.00  0.00           H  
HETATM   88  H31 UNL     1      -1.001  -4.183  -5.604  1.00  0.00           H  
HETATM   89  H32 UNL     1       0.285  -2.136  -2.485  1.00  0.00           H  
HETATM   90  H33 UNL     1       0.867  -0.192  -2.640  1.00  0.00           H  
HETATM   91  H34 UNL     1       1.534  -0.142  -4.292  1.00  0.00           H  
HETATM   92  H35 UNL     1       0.218   2.202  -2.784  1.00  0.00           H  
HETATM   93  H36 UNL     1       1.256   3.810  -2.468  1.00  0.00           H  
HETATM   94  H37 UNL     1       4.610   2.443  -2.284  1.00  0.00           H  
HETATM   95  H38 UNL     1       6.503   3.753  -1.321  1.00  0.00           H  
HETATM   96  H39 UNL     1       6.987   5.974   0.147  1.00  0.00           H  
HETATM   97  H40 UNL     1       6.997   7.140  -1.189  1.00  0.00           H  
HETATM   98  H41 UNL     1       1.659   4.648  -4.698  1.00  0.00           H  
HETATM   99  H42 UNL     1       3.328   3.810  -5.937  1.00  0.00           H  
HETATM  100  H43 UNL     1       0.015   3.012  -4.879  1.00  0.00           H  
HETATM  101  H44 UNL     1       0.863   2.157  -6.599  1.00  0.00           H  
HETATM  102  H45 UNL     1       2.822  -5.117  -0.200  1.00  0.00           H  
HETATM  103  H46 UNL     1       2.603  -3.563  -1.023  1.00  0.00           H  
HETATM  104  H47 UNL     1       4.258  -3.436   0.820  1.00  0.00           H  
HETATM  105  H48 UNL     1       2.997  -3.941   1.959  1.00  0.00           H  
HETATM  106  H49 UNL     1       2.908  -1.358   0.298  1.00  0.00           H  
HETATM  107  H50 UNL     1       1.745  -1.902   1.528  1.00  0.00           H  
HETATM  108  H51 UNL     1       4.712  -1.368   2.005  1.00  0.00           H  
HETATM  109  H52 UNL     1       3.472  -1.915   3.263  1.00  0.00           H  
HETATM  110  H53 UNL     1       3.482   0.645   1.582  1.00  0.00           H  
HETATM  111  H54 UNL     1       2.199   0.200   2.762  1.00  0.00           H  
HETATM  112  H55 UNL     1       4.026   0.112   4.571  1.00  0.00           H  
HETATM  113  H56 UNL     1       5.214   0.612   3.334  1.00  0.00           H  
HETATM  114  H57 UNL     1       4.433   2.458   4.747  1.00  0.00           H  
HETATM  115  H58 UNL     1       2.744   2.165   4.226  1.00  0.00           H  
HETATM  116  H59 UNL     1       3.306   2.633   1.891  1.00  0.00           H  
HETATM  117  H60 UNL     1       5.032   2.911   2.301  1.00  0.00           H  
HETATM  118  H61 UNL     1       2.600   4.437   3.338  1.00  0.00           H  
HETATM  119  H62 UNL     1       4.571   5.997   4.236  1.00  0.00           H  
HETATM  120  H63 UNL     1       5.621   4.563   3.932  1.00  0.00           H  
HETATM  121  H64 UNL     1       4.311   4.472   5.126  1.00  0.00           H  
HETATM  122  H65 UNL     1       3.045   6.111   1.841  1.00  0.00           H  
HETATM  123  H66 UNL     1       3.675   4.680   0.904  1.00  0.00           H  
HETATM  124  H67 UNL     1       4.811   5.790   1.748  1.00  0.00           H  
CONECT    1    2   58   59   60
CONECT    2    3   61   62
CONECT    3    4    5   63
CONECT    4   64   65   66
CONECT    5    6   67   68
CONECT    6    7   69   70
CONECT    7    8   71   72
CONECT    8    9   73   74
CONECT    9   10   75   76
CONECT   10   11   77   78
CONECT   11   12   79   80
CONECT   12   13   81   82
CONECT   13   14   14   15
CONECT   15   16
CONECT   16   17   83   84
CONECT   17   18   44   85
CONECT   18   19   86   87
CONECT   19   20
CONECT   20   21   21   22   23
CONECT   22   88
CONECT   23   24
CONECT   24   25   25   26   27
CONECT   26   89
CONECT   27   28
CONECT   28   29   90   91
CONECT   29   30   42   92
CONECT   30   31
CONECT   31   32   40   93
CONECT   32   33   38
CONECT   33   34   34   94
CONECT   34   35   95
CONECT   35   36   37   37
CONECT   36   96   97
CONECT   37   38
CONECT   38   39   39
CONECT   40   41   42   98
CONECT   41   99
CONECT   42   43  100
CONECT   43  101
CONECT   44   45
CONECT   45   46   46   47
CONECT   47   48  102  103
CONECT   48   49  104  105
CONECT   49   50  106  107
CONECT   50   51  108  109
CONECT   51   52  110  111
CONECT   52   53  112  113
CONECT   53   54  114  115
CONECT   54   55  116  117
CONECT   55   56   57  118
CONECT   56  119  120  121
CONECT   57  122  123  124
END
Download

SMILES for HMDB0116068 (CDP-DG(a-13:0/i-12:0))

[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)CCCCCCCCC(C)C
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INCHI for HMDB0116068 (CDP-DG(a-13:0/i-12:0))

InChI=1S/C37H67N3O15P2/c1-5-28(4)19-15-11-7-9-12-16-20-32(41)50-24-29(53-33(42)21-17-13-8-6-10-14-18-27(2)3)25-51-56(46,47)55-57(48,49)52-26-30-34(43)35(44)36(54-30)40-23-22-31(38)39-37(40)45/h22-23,27-30,34-36,43-44H,5-21,24-26H2,1-4H3,(H,46,47)(H,48,49)(H2,38,39,45)/t28?,29-,30-,34+,35?,36-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Anteisotridecanoyl-2-isododecanoyl-sn-glycero-3-CDPHMDB
1-Anteisotridecanoyl-2-isododecanoyl-sn-glycero-3-cytidine-5'-diphosphateHMDB
CDP-DG(25:0)HMDB
CDP-Diacylglycerol(A-13:0/I-12:0)HMDB
CDP-Diacylglycerol(25:0)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-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinateHMDB
CDP-DG(a-13:0/i-12:0)SMPDB
Chemical FormulaC37H67N3O15P2
Average Molecular Weight855.897
Monoisotopic Molecular Weight855.404742465
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-[(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)-3-[(10-methyldodecanoyl)oxy]-2-[(10-methylundecanoyl)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)CCCCCCCCC(C)C
InChI Identifier
InChI=1S/C37H67N3O15P2/c1-5-28(4)19-15-11-7-9-12-16-20-32(41)50-24-29(53-33(42)21-17-13-8-6-10-14-18-27(2)3)25-51-56(46,47)55-57(48,49)52-26-30-34(43)35(44)36(54-30)40-23-22-31(38)39-37(40)45/h22-23,27-30,34-36,43-44H,5-21,24-26H2,1-4H3,(H,46,47)(H,48,49)(H2,38,39,45)/t28?,29-,30-,34+,35?,36-/m1/s1
InChI KeyURXLTEPIZQRTAV-WXBMFJRSSA-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
logP3.79ALOGPS
logP6.13ChemAxon
logS-4.1ALOGPS
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 Count33ChemAxon
Refractivity207.9 m³·mol⁻¹ChemAxon
Polarizability89.07 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]+260.9830932474
DeepCCS[M-H]-259.15530932474
DeepCCS[M-2H]-292.77730932474
DeepCCS[M+Na]+266.58630932474
AllCCS[M+H]+280.132859911
AllCCS[M+H-H2O]+280.332859911
AllCCS[M+NH4]+279.832859911
AllCCS[M+Na]+279.732859911
AllCCS[M-H]-272.532859911
AllCCS[M+Na-2H]-278.432859911
AllCCS[M+HCOO]-284.932859911

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, 2022.9.18 minutes32390414
Predicted by Siyang on May 30, 202217.5266 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.15 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3230.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid129.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid266.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid170.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid447.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid983.0 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 Acid1001.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)215.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1602.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid892.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1752.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid585.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid526.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate127.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA76.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water23.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CDP-DG(a-13:0/i-12:0)[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)CCCCCCCCC(C)C5494.2Standard polar33892256
CDP-DG(a-13:0/i-12:0)[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)CCCCCCCCC(C)C5054.4Standard non polar33892256
CDP-DG(a-13:0/i-12:0)[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)CCCCCCCCC(C)C5929.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - CDP-DG(a-13:0/i-12:0) 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-12:0) 10V, Positive-QTOFsplash10-03di-0900001010-05d5692ec2fe34bc3f272019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 20V, Positive-QTOFsplash10-03di-1900000000-26dfccccd5c24c482bfc2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 40V, Positive-QTOFsplash10-03di-3910000000-c0053645eec555ada15c2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 10V, Negative-QTOFsplash10-08fs-0920002020-0b8acf9442fc763189c92019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 20V, Negative-QTOFsplash10-03di-4932102010-2b2c7f5100fc351f536b2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 40V, Negative-QTOFsplash10-08i0-4910000000-e3e87cc02f5fc82758ef2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 10V, Negative-QTOFsplash10-0udi-0000000090-54ce03f03c85308f9b6d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 20V, Negative-QTOFsplash10-005c-9410514020-0469ae665adf53929b772021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 40V, Negative-QTOFsplash10-0560-4709403030-71100d43afe8e719ab0b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 10V, Positive-QTOFsplash10-0a4i-1000100390-00a2fb059e8d3addbebf2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 20V, Positive-QTOFsplash10-0pbi-4000000940-5a81b9e3ec908e32b5852021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-13:0/i-12:0) 40V, Positive-QTOFsplash10-000i-0029100000-3a13ebbbc9d916c528572021-09-22Wishart 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 ID74877801
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131822724
PDB IDNot Available
ChEBI ID192156
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