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Showing metabocard for CDP-DG(a-25:0/i-12:0) (HMDB0116139)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-09-09 07:11:33 UTC
Update Date2022-11-30 19:26:29 UTC
HMDB IDHMDB0116139
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(a-25:0/i-12:0)
DescriptionCDP-DG(a-25:0/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-25:0/i-12:0), in particular, consists of one chain of anteisopentacosanoic 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?1563873678
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0116139 (CDP-DG(a-25:0/i-12:0))

CDP-DG(a-25:0/i-12:0)
  Mrv1652309161722292D          

 70 71  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0116139 (CDP-DG(a-25:0/i-12:0))

HMDB0116139
     RDKit          3D
CDP-DG(a-25:0/i-12:0)
160161  0  0  0  0  0  0  0  0999 V2000
    3.5142    7.9624   -2.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7387    7.2575   -2.5157 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8351    7.1986   -1.5098 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0219    6.4741   -2.1051 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4470    6.6328   -0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9309    5.2253   -0.2196 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6376    4.8261    1.2249 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1134    3.4151    1.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8928    3.0591    2.7742 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0116139 (CDP-DG(a-25:0/i-12:0))

CDP-DG(a-25:0/i-12:0)
  Mrv1652309161722292D          

 70 71  0  0  1  0            999 V2000
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 68 69  1  0  0  0  0
 68 70  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0116139

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CCCCCCCCCCCCCCCCCCCCC(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/C49H91N3O15P2/c1-5-40(4)31-27-23-18-16-14-12-10-8-6-7-9-11-13-15-17-19-24-28-32-44(53)62-36-41(65-45(54)33-29-25-21-20-22-26-30-39(2)3)37-63-68(58,59)67-69(60,61)64-38-42-46(55)47(56)48(66-42)52-35-34-43(50)51-49(52)57/h34-35,39-42,46-48,55-56H,5-33,36-38H2,1-4H3,(H,58,59)(H,60,61)(H2,50,51,57)/t40?,41-,42-,46+,47?,48-/m1/s1

> <INCHI_KEY>
FDJMMQLRPKZLPJ-ZHIQHEIOSA-N

> <FORMULA>
C49H91N3O15P2

> <MOLECULAR_WEIGHT>
1024.221

> <EXACT_MASS>
1023.592543238

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
160

> <JCHEM_AVERAGE_POLARIZABILITY>
114.88204241631595

> <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-[(22-methyltetracosanoyl)oxy]-2-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
6.95

> <JCHEM_LOGP>
11.464493966333333

> <ALOGPS_LOGS>
-5.69

> <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>
263.1107

> <JCHEM_ROTATABLE_BOND_COUNT>
45

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.08e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([hydroxy((2R)-3-[(22-methyltetracosanoyl)oxy]-2-[(10-methylundecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0116139 (CDP-DG(a-25:0/i-12:0))

HMDB0116139
     RDKit          3D
CDP-DG(a-25:0/i-12:0)
160161  0  0  0  0  0  0  0  0999 V2000
    3.5142    7.9624   -2.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7387    7.2575   -2.5157 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8351    7.1986   -1.5098 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0219    6.4741   -2.1051 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4470    6.6328   -0.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9309    5.2253   -0.2196 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6376    4.8261    1.2249 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1134    3.4151    1.3387 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8928    3.0591    2.7742 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8860    3.9395    3.4945 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7981    3.5208    4.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3312    2.1277    5.1630 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9065    1.8809    4.7372 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5369    0.4105    4.9380 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7910   -0.0335    6.3353 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4249   -1.4776    6.6180 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1356   -2.3321    5.5857 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0047   -3.8032    5.8182 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6552   -4.5768    4.6610 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8506   -4.4137    3.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5067   -5.0968    2.2320 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7827   -4.3834    1.8695 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4739   -5.0446    0.6895 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6796   -4.2696    0.2604 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3914   -2.9291   -0.2287 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1258   -2.3070   -0.2518 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9799   -1.0093   -0.7775 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5707   -0.5480   -0.6555 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6154   -1.5408   -1.2708 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7186   -2.7449   -0.6225 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3865   -3.8875   -1.2053 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.0386   -3.3561   -2.4475 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4291   -5.3186   -1.5082 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6322   -4.1275   -0.0499 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2579   -2.6685    0.4821 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.8860   -1.9638   -0.7127 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.4314   -2.9467    1.6602 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3143   -2.0451    2.7156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3698   -2.2758    3.7395 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.6591   -2.1326    3.2906 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2147   -3.3617    3.0457 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.5126   -3.4916    1.6587 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7871   -4.6461    1.0320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0688   -4.6959   -0.3174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0715   -3.5362   -1.0510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3552   -3.5397   -2.4426 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7927   -2.3926   -0.3956 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5232   -2.3620    0.9063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2741   -1.2316    1.4282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3545   -4.4085    3.6516 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7776   -5.2976    2.7869 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2934   -3.6262    4.3990 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0471   -4.2077    4.2863 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3962    0.7407   -1.2596 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0354    1.8360   -0.5100 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8694    1.6875    0.7230 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8378    3.1650   -1.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7019    3.1283   -2.6016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4997    2.3328   -3.0470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5189    2.3359   -4.5546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7067    1.6017   -5.1383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0073    2.2324   -4.7505 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1671    1.5031   -5.3069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2396    1.3645   -6.7895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2693    2.6319   -7.5701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3469    2.2420   -9.0553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4977    3.4767   -7.3309 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1866    7.4489   -1.0929 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7541    9.0365   -1.8032 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7061    7.9285   -2.7415 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1002    7.8245   -3.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4500    6.2200   -2.8224 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1977    8.2412   -1.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6462    5.4573   -2.3992 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8780    6.3930   -1.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2878    6.9847   -3.0478 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3265    6.6573    0.4845 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6824    7.2922    0.2837 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9958    5.1247   -0.7808 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7300    4.5361   -0.6006 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8544    5.5253    1.5890 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5441    4.9660    1.8331 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2462    3.2334    0.7113 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9512    2.7515    0.9745 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8944    3.1303    3.2859 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5646    2.0137    2.9127 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9007    3.9193    3.0267 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2671    4.9764    3.4624 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0769    4.1934    5.5012 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7862    3.7179    5.4152 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0190    1.3517    4.7621 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3418    1.9561    6.2824 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1916    2.4643    5.3477 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7465    2.1090    3.6674 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.8974    0.0360    6.5434 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.5042    3.3865   -4.8995 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4207    1.8838   -4.9282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5743    1.6013   -6.2392 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6482    0.5400   -4.8123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0818    2.1677   -3.6335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9978    3.3200   -4.9690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1271    1.9527   -4.9022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1768    0.4698   -4.8863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2371    0.8630   -6.9938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5045    0.6644   -7.2098 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3330    3.2326   -7.4871 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4741    3.1788   -9.6706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4291    1.7600   -9.4109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2451    1.6269   -9.2461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2669    4.4794   -7.7595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7948    3.5776   -6.2883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3327    3.0804   -7.9555 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
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M  END
Download

PDB for HMDB0116139 (CDP-DG(a-25:0/i-12:0))

HEADER    PROTEIN                                 16-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(a-25:0/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      11.184  -8.533   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       9.851  -7.762   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       8.518  -8.533   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       7.185  -7.762   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       5.852  -8.533   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       4.519  -7.762   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       3.185  -8.533   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       1.852  -7.762   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       0.519  -8.533   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -0.814  -7.762   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      -2.147  -8.533   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -3.480  -7.762   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -3.480  -9.302   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -4.813  -8.531   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      28.036 -11.374   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0      28.036 -12.814   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0      26.703 -10.603   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      25.370 -11.374   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      24.037 -10.603   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      22.704 -11.374   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      21.371 -10.603   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      20.038 -11.374   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      18.705 -10.603   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      17.372 -11.374   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      16.038 -10.603   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      14.705 -11.374   0.000  0.00  0.00           C+0
HETATM   70  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   58                                                       
CONECT    7    2                                                            
CONECT    8    4    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8   12                                                       
CONECT   11    8                                                            
CONECT   12   10   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12   23                                                       
CONECT   15   12                                                            
CONECT   16   17   22   20                                                  
CONECT   17   16   18   21                                                  
CONECT   18   19   17   27                                                  
CONECT   19   18   20                                                       
CONECT   20   19   16   23                                                  
CONECT   21   17                                                            
CONECT   22   16                                                            
CONECT   23   14   20                                                       
CONECT   24   25   26                                                       
CONECT   25   24   27   31                                                  
CONECT   26   24   28   30                                                  
CONECT   27   18   25   29                                                  
CONECT   28   26   29                                                       
CONECT   29   27   28                                                       
CONECT   30   26                                                            
CONECT   31   25                                                            
CONECT   32    5   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54   57                                                       
CONECT   57   56                                                            
CONECT   58    6   59   60                                                  
CONECT   59   58                                                            
CONECT   60   58   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69   70                                                  
CONECT   69   68                                                            
CONECT   70   68                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  142    0
END
Download

3D PDB for HMDB0116139 (CDP-DG(a-25:0/i-12:0))

COMPND    HMDB0116139
HETATM    1  C1  UNL     1       3.514   7.962  -2.004  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.739   7.257  -2.516  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.835   7.199  -1.510  1.00  0.00           C  
HETATM    4  C4  UNL     1       7.022   6.474  -2.105  1.00  0.00           C  
HETATM    5  C5  UNL     1       5.447   6.633  -0.172  1.00  0.00           C  
HETATM    6  C6  UNL     1       4.931   5.225  -0.220  1.00  0.00           C  
HETATM    7  C7  UNL     1       4.638   4.826   1.225  1.00  0.00           C  
HETATM    8  C8  UNL     1       4.113   3.415   1.339  1.00  0.00           C  
HETATM    9  C9  UNL     1       3.893   3.059   2.774  1.00  0.00           C  
HETATM   10  C10 UNL     1       2.886   3.940   3.495  1.00  0.00           C  
HETATM   11  C11 UNL     1       2.798   3.521   4.951  1.00  0.00           C  
HETATM   12  C12 UNL     1       2.331   2.128   5.163  1.00  0.00           C  
HETATM   13  C13 UNL     1       0.907   1.881   4.737  1.00  0.00           C  
HETATM   14  C14 UNL     1       0.537   0.411   4.938  1.00  0.00           C  
HETATM   15  C15 UNL     1       0.791  -0.034   6.335  1.00  0.00           C  
HETATM   16  C16 UNL     1       0.425  -1.478   6.618  1.00  0.00           C  
HETATM   17  C17 UNL     1       1.136  -2.332   5.586  1.00  0.00           C  
HETATM   18  C18 UNL     1       1.005  -3.803   5.818  1.00  0.00           C  
HETATM   19  C19 UNL     1       1.655  -4.577   4.661  1.00  0.00           C  
HETATM   20  C20 UNL     1       0.851  -4.414   3.409  1.00  0.00           C  
HETATM   21  C21 UNL     1       1.507  -5.097   2.232  1.00  0.00           C  
HETATM   22  C22 UNL     1       2.783  -4.383   1.870  1.00  0.00           C  
HETATM   23  C23 UNL     1       3.474  -5.045   0.689  1.00  0.00           C  
HETATM   24  C24 UNL     1       4.680  -4.270   0.260  1.00  0.00           C  
HETATM   25  C25 UNL     1       4.391  -2.929  -0.229  1.00  0.00           C  
HETATM   26  O1  UNL     1       5.347  -2.246  -0.680  1.00  0.00           O  
HETATM   27  O2  UNL     1       3.126  -2.307  -0.252  1.00  0.00           O  
HETATM   28  C26 UNL     1       2.980  -1.009  -0.778  1.00  0.00           C  
HETATM   29  C27 UNL     1       1.571  -0.548  -0.656  1.00  0.00           C  
HETATM   30  C28 UNL     1       0.615  -1.541  -1.271  1.00  0.00           C  
HETATM   31  O3  UNL     1       0.719  -2.745  -0.622  1.00  0.00           O  
HETATM   32  P1  UNL     1      -0.386  -3.887  -1.205  1.00  0.00           P  
HETATM   33  O4  UNL     1      -1.039  -3.356  -2.447  1.00  0.00           O  
HETATM   34  O5  UNL     1       0.429  -5.319  -1.508  1.00  0.00           O  
HETATM   35  O6  UNL     1      -1.632  -4.127  -0.050  1.00  0.00           O  
HETATM   36  P2  UNL     1      -2.258  -2.668   0.482  1.00  0.00           P  
HETATM   37  O7  UNL     1      -2.886  -1.964  -0.713  1.00  0.00           O  
HETATM   38  O8  UNL     1      -1.090  -1.646   1.147  1.00  0.00           O  
HETATM   39  O9  UNL     1      -3.431  -2.947   1.660  1.00  0.00           O  
HETATM   40  C29 UNL     1      -3.314  -2.045   2.716  1.00  0.00           C  
HETATM   41  C30 UNL     1      -4.370  -2.276   3.740  1.00  0.00           C  
HETATM   42  O10 UNL     1      -5.659  -2.133   3.291  1.00  0.00           O  
HETATM   43  C31 UNL     1      -6.215  -3.362   3.046  1.00  0.00           C  
HETATM   44  N1  UNL     1      -6.513  -3.492   1.659  1.00  0.00           N  
HETATM   45  C32 UNL     1      -6.787  -4.646   1.032  1.00  0.00           C  
HETATM   46  C33 UNL     1      -7.069  -4.696  -0.317  1.00  0.00           C  
HETATM   47  C34 UNL     1      -7.072  -3.536  -1.051  1.00  0.00           C  
HETATM   48  N2  UNL     1      -7.355  -3.540  -2.443  1.00  0.00           N  
HETATM   49  N3  UNL     1      -6.793  -2.393  -0.396  1.00  0.00           N  
HETATM   50  C35 UNL     1      -6.523  -2.362   0.906  1.00  0.00           C  
HETATM   51  O11 UNL     1      -6.274  -1.232   1.428  1.00  0.00           O  
HETATM   52  C36 UNL     1      -5.355  -4.408   3.652  1.00  0.00           C  
HETATM   53  O12 UNL     1      -4.778  -5.298   2.787  1.00  0.00           O  
HETATM   54  C37 UNL     1      -4.293  -3.626   4.399  1.00  0.00           C  
HETATM   55  O13 UNL     1      -3.047  -4.208   4.286  1.00  0.00           O  
HETATM   56  O14 UNL     1       1.396   0.741  -1.260  1.00  0.00           O  
HETATM   57  C38 UNL     1       1.035   1.836  -0.510  1.00  0.00           C  
HETATM   58  O15 UNL     1       0.869   1.688   0.723  1.00  0.00           O  
HETATM   59  C39 UNL     1       0.838   3.165  -1.096  1.00  0.00           C  
HETATM   60  C40 UNL     1       0.702   3.128  -2.602  1.00  0.00           C  
HETATM   61  C41 UNL     1      -0.500   2.333  -3.047  1.00  0.00           C  
HETATM   62  C42 UNL     1      -0.519   2.336  -4.555  1.00  0.00           C  
HETATM   63  C43 UNL     1      -1.707   1.602  -5.138  1.00  0.00           C  
HETATM   64  C44 UNL     1      -3.007   2.232  -4.751  1.00  0.00           C  
HETATM   65  C45 UNL     1      -4.167   1.503  -5.307  1.00  0.00           C  
HETATM   66  C46 UNL     1      -4.240   1.365  -6.790  1.00  0.00           C  
HETATM   67  C47 UNL     1      -4.269   2.632  -7.570  1.00  0.00           C  
HETATM   68  C48 UNL     1      -4.347   2.242  -9.055  1.00  0.00           C  
HETATM   69  C49 UNL     1      -5.498   3.477  -7.331  1.00  0.00           C  
HETATM   70  H1  UNL     1       3.187   7.449  -1.093  1.00  0.00           H  
HETATM   71  H2  UNL     1       3.754   9.037  -1.803  1.00  0.00           H  
HETATM   72  H3  UNL     1       2.706   7.928  -2.741  1.00  0.00           H  
HETATM   73  H4  UNL     1       5.100   7.825  -3.393  1.00  0.00           H  
HETATM   74  H5  UNL     1       4.450   6.220  -2.822  1.00  0.00           H  
HETATM   75  H6  UNL     1       6.198   8.241  -1.307  1.00  0.00           H  
HETATM   76  H7  UNL     1       6.646   5.457  -2.399  1.00  0.00           H  
HETATM   77  H8  UNL     1       7.878   6.393  -1.412  1.00  0.00           H  
HETATM   78  H9  UNL     1       7.288   6.985  -3.048  1.00  0.00           H  
HETATM   79  H10 UNL     1       6.326   6.657   0.484  1.00  0.00           H  
HETATM   80  H11 UNL     1       4.682   7.292   0.284  1.00  0.00           H  
HETATM   81  H12 UNL     1       3.996   5.125  -0.781  1.00  0.00           H  
HETATM   82  H13 UNL     1       5.730   4.536  -0.601  1.00  0.00           H  
HETATM   83  H14 UNL     1       3.854   5.525   1.589  1.00  0.00           H  
HETATM   84  H15 UNL     1       5.544   4.966   1.833  1.00  0.00           H  
HETATM   85  H16 UNL     1       3.246   3.233   0.711  1.00  0.00           H  
HETATM   86  H17 UNL     1       4.951   2.752   0.974  1.00  0.00           H  
HETATM   87  H18 UNL     1       4.894   3.130   3.286  1.00  0.00           H  
HETATM   88  H19 UNL     1       3.565   2.014   2.913  1.00  0.00           H  
HETATM   89  H20 UNL     1       1.901   3.919   3.027  1.00  0.00           H  
HETATM   90  H21 UNL     1       3.267   4.976   3.462  1.00  0.00           H  
HETATM   91  H22 UNL     1       2.077   4.193   5.501  1.00  0.00           H  
HETATM   92  H23 UNL     1       3.786   3.718   5.415  1.00  0.00           H  
HETATM   93  H24 UNL     1       3.019   1.352   4.762  1.00  0.00           H  
HETATM   94  H25 UNL     1       2.342   1.956   6.282  1.00  0.00           H  
HETATM   95  H26 UNL     1       0.192   2.464   5.348  1.00  0.00           H  
HETATM   96  H27 UNL     1       0.747   2.109   3.667  1.00  0.00           H  
HETATM   97  H28 UNL     1      -0.511   0.233   4.660  1.00  0.00           H  
HETATM   98  H29 UNL     1       1.187  -0.143   4.203  1.00  0.00           H  
HETATM   99  H30 UNL     1       0.289   0.655   7.060  1.00  0.00           H  
HETATM  100  H31 UNL     1       1.897   0.036   6.543  1.00  0.00           H  
HETATM  101  H32 UNL     1      -0.669  -1.578   6.510  1.00  0.00           H  
HETATM  102  H33 UNL     1       0.770  -1.698   7.650  1.00  0.00           H  
HETATM  103  H34 UNL     1       2.227  -2.086   5.632  1.00  0.00           H  
HETATM  104  H35 UNL     1       0.733  -2.077   4.593  1.00  0.00           H  
HETATM  105  H36 UNL     1       1.439  -4.109   6.777  1.00  0.00           H  
HETATM  106  H37 UNL     1      -0.063  -4.132   5.808  1.00  0.00           H  
HETATM  107  H38 UNL     1       2.693  -4.216   4.544  1.00  0.00           H  
HETATM  108  H39 UNL     1       1.684  -5.635   5.013  1.00  0.00           H  
HETATM  109  H40 UNL     1       0.625  -3.348   3.163  1.00  0.00           H  
HETATM  110  H41 UNL     1      -0.150  -4.907   3.632  1.00  0.00           H  
HETATM  111  H42 UNL     1       0.853  -5.177   1.348  1.00  0.00           H  
HETATM  112  H43 UNL     1       1.766  -6.135   2.610  1.00  0.00           H  
HETATM  113  H44 UNL     1       2.586  -3.325   1.708  1.00  0.00           H  
HETATM  114  H45 UNL     1       3.482  -4.446   2.741  1.00  0.00           H  
HETATM  115  H46 UNL     1       2.783  -5.214  -0.154  1.00  0.00           H  
HETATM  116  H47 UNL     1       3.745  -6.069   1.056  1.00  0.00           H  
HETATM  117  H48 UNL     1       5.392  -4.197   1.125  1.00  0.00           H  
HETATM  118  H49 UNL     1       5.217  -4.852  -0.518  1.00  0.00           H  
HETATM  119  H50 UNL     1       3.663  -0.362  -0.151  1.00  0.00           H  
HETATM  120  H51 UNL     1       3.327  -1.029  -1.835  1.00  0.00           H  
HETATM  121  H52 UNL     1       1.357  -0.410   0.426  1.00  0.00           H  
HETATM  122  H53 UNL     1      -0.387  -1.146  -1.416  1.00  0.00           H  
HETATM  123  H54 UNL     1       0.979  -1.748  -2.339  1.00  0.00           H  
HETATM  124  H55 UNL     1       0.115  -6.071  -0.941  1.00  0.00           H  
HETATM  125  H56 UNL     1      -1.432  -0.744   1.273  1.00  0.00           H  
HETATM  126  H57 UNL     1      -2.320  -2.168   3.205  1.00  0.00           H  
HETATM  127  H58 UNL     1      -3.415  -1.014   2.335  1.00  0.00           H  
HETATM  128  H59 UNL     1      -4.231  -1.457   4.514  1.00  0.00           H  
HETATM  129  H60 UNL     1      -7.200  -3.396   3.600  1.00  0.00           H  
HETATM  130  H61 UNL     1      -6.783  -5.553   1.619  1.00  0.00           H  
HETATM  131  H62 UNL     1      -7.280  -5.678  -0.758  1.00  0.00           H  
HETATM  132  H63 UNL     1      -7.199  -4.357  -3.070  1.00  0.00           H  
HETATM  133  H64 UNL     1      -7.746  -2.682  -2.899  1.00  0.00           H  
HETATM  134  H65 UNL     1      -5.878  -5.018   4.441  1.00  0.00           H  
HETATM  135  H66 UNL     1      -4.245  -5.934   3.362  1.00  0.00           H  
HETATM  136  H67 UNL     1      -4.557  -3.477   5.466  1.00  0.00           H  
HETATM  137  H68 UNL     1      -2.400  -3.609   4.758  1.00  0.00           H  
HETATM  138  H69 UNL     1       1.629   3.895  -0.857  1.00  0.00           H  
HETATM  139  H70 UNL     1      -0.113   3.587  -0.705  1.00  0.00           H  
HETATM  140  H71 UNL     1       1.623   2.774  -3.085  1.00  0.00           H  
HETATM  141  H72 UNL     1       0.530   4.178  -2.948  1.00  0.00           H  
HETATM  142  H73 UNL     1      -1.400   2.947  -2.747  1.00  0.00           H  
HETATM  143  H74 UNL     1      -0.581   1.344  -2.603  1.00  0.00           H  
HETATM  144  H75 UNL     1      -0.504   3.386  -4.900  1.00  0.00           H  
HETATM  145  H76 UNL     1       0.421   1.884  -4.928  1.00  0.00           H  
HETATM  146  H77 UNL     1      -1.574   1.601  -6.239  1.00  0.00           H  
HETATM  147  H78 UNL     1      -1.648   0.540  -4.812  1.00  0.00           H  
HETATM  148  H79 UNL     1      -3.082   2.168  -3.634  1.00  0.00           H  
HETATM  149  H80 UNL     1      -2.998   3.320  -4.969  1.00  0.00           H  
HETATM  150  H81 UNL     1      -5.127   1.953  -4.902  1.00  0.00           H  
HETATM  151  H82 UNL     1      -4.177   0.470  -4.886  1.00  0.00           H  
HETATM  152  H83 UNL     1      -5.237   0.863  -6.994  1.00  0.00           H  
HETATM  153  H84 UNL     1      -3.505   0.664  -7.210  1.00  0.00           H  
HETATM  154  H85 UNL     1      -3.333   3.233  -7.487  1.00  0.00           H  
HETATM  155  H86 UNL     1      -4.474   3.179  -9.671  1.00  0.00           H  
HETATM  156  H87 UNL     1      -3.429   1.760  -9.411  1.00  0.00           H  
HETATM  157  H88 UNL     1      -5.245   1.627  -9.246  1.00  0.00           H  
HETATM  158  H89 UNL     1      -5.267   4.479  -7.759  1.00  0.00           H  
HETATM  159  H90 UNL     1      -5.795   3.578  -6.288  1.00  0.00           H  
HETATM  160  H91 UNL     1      -6.333   3.080  -7.956  1.00  0.00           H  
CONECT    1    2   70   71   72
CONECT    2    3   73   74
CONECT    3    4    5   75
CONECT    4   76   77   78
CONECT    5    6   79   80
CONECT    6    7   81   82
CONECT    7    8   83   84
CONECT    8    9   85   86
CONECT    9   10   87   88
CONECT   10   11   89   90
CONECT   11   12   91   92
CONECT   12   13   93   94
CONECT   13   14   95   96
CONECT   14   15   97   98
CONECT   15   16   99  100
CONECT   16   17  101  102
CONECT   17   18  103  104
CONECT   18   19  105  106
CONECT   19   20  107  108
CONECT   20   21  109  110
CONECT   21   22  111  112
CONECT   22   23  113  114
CONECT   23   24  115  116
CONECT   24   25  117  118
CONECT   25   26   26   27
CONECT   27   28
CONECT   28   29  119  120
CONECT   29   30   56  121
CONECT   30   31  122  123
CONECT   31   32
CONECT   32   33   33   34   35
CONECT   34  124
CONECT   35   36
CONECT   36   37   37   38   39
CONECT   38  125
CONECT   39   40
CONECT   40   41  126  127
CONECT   41   42   54  128
CONECT   42   43
CONECT   43   44   52  129
CONECT   44   45   50
CONECT   45   46   46  130
CONECT   46   47  131
CONECT   47   48   49   49
CONECT   48  132  133
CONECT   49   50
CONECT   50   51   51
CONECT   52   53   54  134
CONECT   53  135
CONECT   54   55  136
CONECT   55  137
CONECT   56   57
CONECT   57   58   58   59
CONECT   59   60  138  139
CONECT   60   61  140  141
CONECT   61   62  142  143
CONECT   62   63  144  145
CONECT   63   64  146  147
CONECT   64   65  148  149
CONECT   65   66  150  151
CONECT   66   67  152  153
CONECT   67   68   69  154
CONECT   68  155  156  157
CONECT   69  158  159  160
END
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SMILES for HMDB0116139 (CDP-DG(a-25:0/i-12:0))

[H][C@@](COC(=O)CCCCCCCCCCCCCCCCCCCCC(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 HMDB0116139 (CDP-DG(a-25:0/i-12:0))

InChI=1S/C49H91N3O15P2/c1-5-40(4)31-27-23-18-16-14-12-10-8-6-7-9-11-13-15-17-19-24-28-32-44(53)62-36-41(65-45(54)33-29-25-21-20-22-26-30-39(2)3)37-63-68(58,59)67-69(60,61)64-38-42-46(55)47(56)48(66-42)52-35-34-43(50)51-49(52)57/h34-35,39-42,46-48,55-56H,5-33,36-38H2,1-4H3,(H,58,59)(H,60,61)(H2,50,51,57)/t40?,41-,42-,46+,47?,48-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Anteisopentacosanoyl-2-isododecanoyl-sn-glycero-3-CDPHMDB
1-Anteisopentacosanoyl-2-isododecanoyl-sn-glycero-3-cytidine-5'-diphosphateHMDB
CDP-DG(37:0)HMDB
CDP-Diacylglycerol(A-25:0/I-12:0)HMDB
CDP-Diacylglycerol(37:0)HMDB
{[(2R,3R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(22-methyltetracosanoyl)oxy]-2-[(10-methylundecanoyl)oxy]propoxy]phosphoryl}oxy)phosphinateHMDB
CDP-DG(a-25:0/i-12:0)SMPDB
Chemical FormulaC49H91N3O15P2
Average Molecular Weight1024.221
Monoisotopic Molecular Weight1023.592543238
IUPAC Name{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(2R)-3-[(22-methyltetracosanoyl)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-[(22-methyltetracosanoyl)oxy]-2-[(10-methylundecanoyl)oxy]propoxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCCCCCCCCCC(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/C49H91N3O15P2/c1-5-40(4)31-27-23-18-16-14-12-10-8-6-7-9-11-13-15-17-19-24-28-32-44(53)62-36-41(65-45(54)33-29-25-21-20-22-26-30-39(2)3)37-63-68(58,59)67-69(60,61)64-38-42-46(55)47(56)48(66-42)52-35-34-43(50)51-49(52)57/h34-35,39-42,46-48,55-56H,5-33,36-38H2,1-4H3,(H,58,59)(H,60,61)(H2,50,51,57)/t40?,41-,42-,46+,47?,48-/m1/s1
InChI KeyFDJMMQLRPKZLPJ-ZHIQHEIOSA-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
logP6.95ALOGPS
logP11.46ChemAxon
logS-5.7ALOGPS
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 Count45ChemAxon
Refractivity263.11 m³·mol⁻¹ChemAxon
Polarizability114.88 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]+255.76730932474
DeepCCS[M-H]-253.94330932474
DeepCCS[M-2H]-287.62630932474
DeepCCS[M+Na]+261.77530932474
AllCCS[M+H]+313.432859911
AllCCS[M+H-H2O]+313.632859911
AllCCS[M+NH4]+313.232859911
AllCCS[M+Na]+313.132859911
AllCCS[M-H]-303.932859911
AllCCS[M+Na-2H]-310.332859911
AllCCS[M+HCOO]-317.332859911

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, 2022.10.65 minutes32390414
Predicted by Siyang on May 30, 202225.4922 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.04 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4884.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid164.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid353.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid180.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1028.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1525.6 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 Acid1438.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)250.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2609.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1214.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2613.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1042.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid698.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate154.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA249.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water9.3 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - CDP-DG(a-25:0/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-25:0/i-12:0) 10V, Positive-QTOFsplash10-03di-1900000000-938799598c99060c80d42019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 20V, Positive-QTOFsplash10-03di-2901000100-30f408ffc106f1484fbc2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 40V, Positive-QTOFsplash10-03di-3900100000-30689f674ec657de0edc2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 10V, Negative-QTOFsplash10-08n9-1906000011-4332f11d4b8cb1dd354c2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 20V, Negative-QTOFsplash10-03e9-5709100100-64df160cd0a469d1a7452019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 40V, Negative-QTOFsplash10-0bvi-4902000000-43fc7878a2da5635ca7c2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 10V, Negative-QTOFsplash10-00di-9000000010-0c05077621430223e0052021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 20V, Negative-QTOFsplash10-005c-9202410020-7f094403c16a525b17222021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 40V, Negative-QTOFsplash10-1031-8609122010-17937730d8fedd9d37f72021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 10V, Positive-QTOFsplash10-00di-9100001021-7c08e0f680c350e8c8ae2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 20V, Positive-QTOFsplash10-0ab9-9000000161-0e406e562d1c0d9527a92021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(a-25:0/i-12:0) 40V, Positive-QTOFsplash10-0079-1029220000-a4e9b7c9cf458d4d06062021-09-24Wishart 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 ID74877852
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131822795
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