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Showing metabocard for CDP-DG(i-13:0/PGE2) (HMDB0293387)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 14:11:40 UTC
Update Date2022-11-30 20:08:34 UTC
HMDB IDHMDB0293387
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(i-13:0/PGE2)
DescriptionCDP-DG(i-13:0/PGE2) is an oxidized CDP-diacylglycerol (CDP-DG). Oxidized CDP-diacylglycerols are glycerophospholipids in which a cytidine diphosphate moiety occupies a glycerol substitution site and at least one of the fatty acyl chains has undergone oxidation. As all oxidized lipids, oxidized CDP-diacylglycerols belong to a group of biomolecules that have a role as signaling molecules. The biosynthesis of oxidized lipids is mediated by several enzymatic families, including cyclooxygenases (COX), lipoxygenases (LOX) and cytochrome P450s (CYP). Non-enzymatically oxidized lipids are produced by uncontrolled oxidation through free radicals and are considered harmful to human health (PMID: 33329396 ). As is the case with diacylglycerols, CDP-diacylglycerols can have many different combinations of fatty acids of varying lengths, saturation and degrees of oxidation attached at the C-1 and C-2 positions. CDP-DG(i-13:0/PGE2), in particular, consists of one chain of one 11-methyldodecanoyl at the C-1 position and one chain of Prostaglandin E2 at the C-2 position. Phospholipids are ubiquitous in nature and are key components of the lipid bilayer of cells, as well as being involved in metabolism and signaling. Similarly to what occurs with phospholipids, the fatty acid distribution at the C-1 and C-2 positions of glycerol within oxidized phospholipids is continually in flux, owing to phospholipid degradation and the continuous phospholipid remodeling that occurs while these molecules are in membranes. Oxidized CDP-DGs can be synthesized via three different routes. In one route, the oxidized CDP-DG is synthetized de novo following the same mechanisms as for CDP-DGs but incorporating oxidized acyl chains (PMID: 33329396 ). An alternative is the transacylation of one of the non-oxidized acyl chains with an oxidized acylCoA (PMID: 33329396 ). The third pathway results from the oxidation of the acyl chain while still attached to the CDP-DG backbone, mainly through the action of LOX (PMID: 33329396 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0293387 (CDP-DG(i-13:0/PGE2))


  Mrv1652309172116122D          

 68 70  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0293387 (CDP-DG(i-13:0/PGE2))

HMDB0293387
     RDKit          3D
CDP-DG(i-13:0/PGE2)
143145  0  0  0  0  0  0  0  0999 V2000
  -12.0777    4.7661   -0.5516 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6316    3.4974   -1.2007 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5675    2.7601   -0.3824 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0839    2.3978    0.9680 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1274    1.6625    1.8340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8797    2.3427    2.2574 C   0  0  2  0  0  0  0  0  0  0  0  0
   -9.3007    3.5037    2.9773 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0293387 (CDP-DG(i-13:0/PGE2))


  Mrv1652309172116122D          

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M  END
> <DATABASE_ID>
HMDB0293387

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC[C@H](O)C=C[C@H]1[C@H](O)CC(=O)[C@@H]2CC=CCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(O)(=O)OP(O)(=O)OC[C@@H](O[C@H]2N2C=CC(N)=NC2=O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C45H75N3O18P2/c1-4-5-13-19-32(49)23-24-34-36(50)27-37(51)35-20-15-11-12-17-22-41(53)64-33(28-61-40(52)21-16-10-8-6-7-9-14-18-31(2)3)29-62-67(57,58)66-68(59,60)63-30-38(43(55)42(34)54)65-44(35)48-26-25-39(46)47-45(48)56/h11,15,23-26,31-36,38,42-44,49-50,54-55H,4-10,12-14,16-22,27-30H2,1-3H3,(H,57,58)(H,59,60)(H2,46,47,56)/b15-11-,24-23-/t32-,33+,34-,35-,36+,38+,42-,43+,44+/m0/s1

> <INCHI_KEY>
FDTZDJCTGRIIDS-BVOVXBNSSA-N

> <FORMULA>
C45H75N3O18P2

> <MOLECULAR_WEIGHT>
1008.046

> <EXACT_MASS>
1007.452086583

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
143

> <JCHEM_AVERAGE_POLARIZABILITY>
105.64341382156586

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1R,9R,15Z,18R,21R,22S,23S,24S,26R)-26-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,21,23,24-pentahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,19-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacos-15-en-9-yl]methyl 11-methyldodecanoate

> <ALOGPS_LOGP>
2.49

> <JCHEM_LOGP>
4.783204840982964

> <ALOGPS_LOGS>
-3.53

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2718999239461373

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8697147678387385

> <JCHEM_PKA_STRONGEST_BASIC>
0.3038794608558414

> <JCHEM_POLAR_SURFACE_AREA>
320.8

> <JCHEM_REFRACTIVITY>
248.76180000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.01e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,9R,15Z,18R,21R,22S,23S,24S,26R)-26-(4-amino-2-oxopyrimidin-1-yl)-4,6,21,23,24-pentahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,19-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacos-15-en-9-yl]methyl 11-methyldodecanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0293387 (CDP-DG(i-13:0/PGE2))

HMDB0293387
     RDKit          3D
CDP-DG(i-13:0/PGE2)
143145  0  0  0  0  0  0  0  0999 V2000
  -12.0777    4.7661   -0.5516 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6316    3.4974   -1.2007 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5675    2.7601   -0.3824 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0839    2.3978    0.9680 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1274    1.6625    1.8340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8797    2.3427    2.2574 C   0  0  2  0  0  0  0  0  0  0  0  0
   -9.3007    3.5037    2.9773 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9220    2.7484    1.2327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0285    1.9860    0.6384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8665    0.5166    0.9577 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.5461    0.4141    1.6528 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.5431    1.2199    1.0810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0929   -0.9601    2.0086 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.2995   -1.2292    3.3863 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6247   -1.1845    1.7160 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8960   -1.1076    3.0849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5417   -1.4224    2.9384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7249   -0.2306    2.0520 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.3656    1.0958    2.4606 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9617   -0.5470    0.4206 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8837   -0.2115    2.5000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6083   -1.6723    2.0574 P   0  0  0  0  0  5  0  0  0  0  0  0
    0.5899   -2.7480    1.7868 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6104   -2.1211    3.3627 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6107   -1.3736    0.7208 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6270   -0.5533    1.1108 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2089    0.3308    0.0223 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.6950    0.0148   -0.1437 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4472    0.9745   -0.7673 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4080    1.5070   -1.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4410    0.9712   -2.7423 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2046    2.5360   -2.6590 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4635    3.0593   -2.2033 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6323    3.8059   -0.9615 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3690    3.0929    0.3205 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2430    1.8806    0.4059 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0727    1.0956    1.6794 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9338   -0.1446    1.6808 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3766    0.2308    1.5390 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2208   -1.0487    1.5226 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6588   -0.6105    1.3715 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8346    0.1780    0.0802 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.5063   -1.8816    1.2615 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5100    0.4650   -1.1173 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4704    0.9369   -1.7528 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3974    2.0971   -2.3257 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1879    0.1786   -1.9108 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9164   -0.0442   -3.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3950   -0.8050   -3.4660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4892    0.0958   -3.0161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7466   -0.2721   -2.8557 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0854   -1.6449   -2.4016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8154   -1.6521   -1.0585 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.2755   -1.6217   -1.3261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8483   -2.6591   -1.5889 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0856   -0.3718   -1.2883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1189   -0.3164   -0.2319 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.6067   -1.5810    0.1405 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3374   -2.6790   -0.1142 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9025   -4.0067   -0.2556 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9271   -4.6285   -1.4381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4828   -5.9005   -1.4885 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9937   -6.5020   -0.3512 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5687   -7.8074   -0.3858 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9557   -5.8563    0.8202 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4029   -4.6126    0.8289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4083   -4.0769    1.9913 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2570   -2.3448    1.1958 O   0  0  0  0  0  0  0  0  0  0  0  0
  -13.0398    4.6193   -0.0072 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3435    5.1423    0.1662 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2231    5.5983   -1.3011 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4622    2.7805   -1.3712 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1630    3.7228   -2.1819 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3636    1.8294   -0.9883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6608    3.3415   -0.3667 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3817    3.3523    1.5018 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0772    1.8567    0.8924 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7146    1.3047    2.7495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8531    0.7127    1.2978 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3623    1.7540    3.0856 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1783    3.3413    3.4058 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9169    3.8175    0.9385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3723    2.4367   -0.1227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6297    0.2908    1.7220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7119    0.9535    2.6442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6355    2.1762    1.3267 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7388   -1.6888    1.4959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0487   -1.8398    3.5213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2543   -0.2386    1.2278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9523   -0.0885    3.4888 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3193   -1.8020    3.8060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4876   -1.3934    0.2270 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0477   -2.5190    4.0990 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3607    0.0616    1.9977 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4696   -1.2399    1.4329 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2593    1.3593    0.5445 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0865   -0.1625    0.8978 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8315   -0.9463   -0.6843 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3294    2.1391   -3.7457 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4918    3.4323   -2.9175 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2375    2.1952   -2.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9005    3.7184   -3.0560 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6630    4.2890   -0.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9074    4.7043   -0.9714 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3210    2.9257    0.4811 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7576    3.8097    1.1563 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1432    1.2273   -0.4865 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3230    2.2309    0.3801 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0165    0.8358    1.8926 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4307    1.7302    2.5283 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6087   -0.8099    0.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.8031   -0.6418    2.6643 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.6238    0.7608    0.6164 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.6922    0.7987    2.4379 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1151   -1.5957    2.4566 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.9205   -1.6813    0.6668 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.9785   -0.0184    2.2346 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8185    0.0315   -0.3753 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.0456   -0.1375   -0.6473 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6936    1.2750    0.2631 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8811   -2.7915    1.4531 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8750   -1.9782    0.2194 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.3145   -1.8892    2.0228 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1509   -0.7737   -1.3969 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3250    0.7929   -1.5688 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7065   -0.7086   -3.8150 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8176    0.9214   -3.9076 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.2157   -8.5132    0.2690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3246   -7.9586   -1.0896 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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  1 70  1  0
  1 71  1  0
  2 72  1  0
  2 73  1  0
  3 74  1  0
  3 75  1  0
  4 76  1  0
  4 77  1  0
  5 78  1  0
  5 79  1  0
  6 80  1  1
  7 81  1  0
  8 82  1  0
  9 83  1  0
 10 84  1  1
 11 85  1  1
 12 86  1  0
 13 87  1  6
 14 88  1  0
 15 89  1  6
 16 90  1  0
 16 91  1  0
 20 92  1  0
 24 93  1  0
 26 94  1  0
 26 95  1  0
 27 96  1  1
 28 97  1  0
 28 98  1  0
 32 99  1  0
 32100  1  0
 33101  1  0
 33102  1  0
 34103  1  0
 34104  1  0
 35105  1  0
 35106  1  0
 36107  1  0
 36108  1  0
 37109  1  0
 37110  1  0
 38111  1  0
 38112  1  0
 39113  1  0
 39114  1  0
 40115  1  0
 40116  1  0
 41117  1  0
 42118  1  0
 42119  1  0
 42120  1  0
 43121  1  0
 43122  1  0
 43123  1  0
 47124  1  0
 47125  1  0
 48126  1  0
 48127  1  0
 49128  1  0
 49129  1  0
 50130  1  0
 51131  1  0
 52132  1  0
 52133  1  0
 53134  1  1
 56135  1  0
 56136  1  0
 57137  1  6
 58138  1  0
 59139  1  6
 61140  1  0
 62141  1  0
 64142  1  0
 64143  1  0
M  END
Download

PDB for HMDB0293387 (CDP-DG(i-13:0/PGE2))

HEADER    PROTEIN                                 17-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-21         0                                  
HETATM    1  N   UNK     0      -6.240  -2.459   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -4.960  -1.504   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -5.282   0.002   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -4.139   1.034   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -5.388   2.062   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -2.674   0.560   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -2.352  -0.946   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.495  -1.978   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.531   1.592   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.334   2.972   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.292   4.593   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.780   4.688   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.895   6.571   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       0.010   7.867   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0      -1.528   8.613   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -0.455   9.583   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.537   8.346   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       3.070   7.963   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       3.654   9.580   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       2.499   9.556   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.456   7.159   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       5.570   6.023   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.883   4.465   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.560   5.117   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.622   6.657   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.075   7.495   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      10.564   9.027   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      11.329   6.567   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.810   7.025   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      13.593   5.662   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      14.978   6.369   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      15.957   5.147   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      17.362   5.834   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      18.498   4.750   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      20.012   5.156   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      21.367   4.352   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      22.763   5.117   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      23.983   4.128   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      23.076   6.669   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       6.696   3.102   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0       7.373   1.671   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       8.980   1.285   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       7.714   0.120   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       6.622  -1.024   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       5.158  -1.668   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       3.554  -1.765   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       2.014  -1.370   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       0.523  -0.784   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -0.228   0.644   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       1.224   1.273   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       2.544   0.410   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0       2.635   1.959   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       3.019   3.484   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0       4.358   2.537   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0       1.959   4.572   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0       3.277   5.305   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       4.505   6.258   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       5.786   7.529   0.000  0.00  0.00           C+0
HETATM   59  O   UNK     0       7.129   6.339   0.000  0.00  0.00           O+0
HETATM   60  C   UNK     0       6.447   9.225   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       7.051  10.785   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       6.582  12.344   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       7.444  13.633   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0       6.762  15.014   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      -1.035   5.581   0.000  0.00  0.00           C+0
HETATM   66  O   UNK     0      -2.273   6.945   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0       0.661   5.481   0.000  0.00  0.00           C+0
HETATM   68  O   UNK     0       0.900   7.029   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    2                                                       
CONECT    9    6   10   49                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   65                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14   18                                                       
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   40                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37                                                            
CONECT   40   23   41                                                       
CONECT   41   40   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48    9   50                                                  
CONECT   50   49   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50   53                                                       
CONECT   53   52   54   55                                                  
CONECT   54   53                                                            
CONECT   55   53   56   67                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59   60                                                  
CONECT   59   58                                                            
CONECT   60   58   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63                                                            
CONECT   65   11   66   67                                                  
CONECT   66   65                                                            
CONECT   67   65   55   68                                                  
CONECT   68   67                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  140    0
END
Download

3D PDB for HMDB0293387 (CDP-DG(i-13:0/PGE2))

COMPND    HMDB0293387
HETATM    1  C1  UNL     1     -12.078   4.766  -0.552  1.00  0.00           C  
HETATM    2  C2  UNL     1     -11.632   3.497  -1.201  1.00  0.00           C  
HETATM    3  C3  UNL     1     -10.567   2.760  -0.382  1.00  0.00           C  
HETATM    4  C4  UNL     1     -11.084   2.398   0.968  1.00  0.00           C  
HETATM    5  C5  UNL     1     -10.127   1.663   1.834  1.00  0.00           C  
HETATM    6  C6  UNL     1      -8.880   2.343   2.257  1.00  0.00           C  
HETATM    7  O1  UNL     1      -9.301   3.504   2.977  1.00  0.00           O  
HETATM    8  C7  UNL     1      -7.922   2.748   1.233  1.00  0.00           C  
HETATM    9  C8  UNL     1      -7.029   1.986   0.638  1.00  0.00           C  
HETATM   10  C9  UNL     1      -6.866   0.517   0.958  1.00  0.00           C  
HETATM   11  C10 UNL     1      -5.546   0.414   1.653  1.00  0.00           C  
HETATM   12  O2  UNL     1      -4.543   1.220   1.081  1.00  0.00           O  
HETATM   13  C11 UNL     1      -5.093  -0.960   2.009  1.00  0.00           C  
HETATM   14  O3  UNL     1      -5.299  -1.229   3.386  1.00  0.00           O  
HETATM   15  C12 UNL     1      -3.625  -1.185   1.716  1.00  0.00           C  
HETATM   16  C13 UNL     1      -2.896  -1.108   3.085  1.00  0.00           C  
HETATM   17  O4  UNL     1      -1.542  -1.422   2.938  1.00  0.00           O  
HETATM   18  P1  UNL     1      -0.725  -0.231   2.052  1.00  0.00           P  
HETATM   19  O5  UNL     1      -1.366   1.096   2.461  1.00  0.00           O  
HETATM   20  O6  UNL     1      -0.962  -0.547   0.421  1.00  0.00           O  
HETATM   21  O7  UNL     1       0.884  -0.212   2.500  1.00  0.00           O  
HETATM   22  P2  UNL     1       1.608  -1.672   2.057  1.00  0.00           P  
HETATM   23  O8  UNL     1       0.590  -2.748   1.787  1.00  0.00           O  
HETATM   24  O9  UNL     1       2.610  -2.121   3.363  1.00  0.00           O  
HETATM   25  O10 UNL     1       2.611  -1.374   0.721  1.00  0.00           O  
HETATM   26  C14 UNL     1       3.627  -0.553   1.111  1.00  0.00           C  
HETATM   27  C15 UNL     1       4.209   0.331   0.022  1.00  0.00           C  
HETATM   28  C16 UNL     1       5.695   0.015  -0.144  1.00  0.00           C  
HETATM   29  O11 UNL     1       6.447   0.975  -0.767  1.00  0.00           O  
HETATM   30  C17 UNL     1       6.408   1.507  -1.998  1.00  0.00           C  
HETATM   31  O12 UNL     1       5.441   0.971  -2.742  1.00  0.00           O  
HETATM   32  C18 UNL     1       7.205   2.536  -2.659  1.00  0.00           C  
HETATM   33  C19 UNL     1       8.464   3.059  -2.203  1.00  0.00           C  
HETATM   34  C20 UNL     1       8.632   3.806  -0.961  1.00  0.00           C  
HETATM   35  C21 UNL     1       8.369   3.093   0.320  1.00  0.00           C  
HETATM   36  C22 UNL     1       9.243   1.881   0.406  1.00  0.00           C  
HETATM   37  C23 UNL     1       9.073   1.096   1.679  1.00  0.00           C  
HETATM   38  C24 UNL     1       9.934  -0.145   1.681  1.00  0.00           C  
HETATM   39  C25 UNL     1      11.377   0.231   1.539  1.00  0.00           C  
HETATM   40  C26 UNL     1      12.221  -1.049   1.523  1.00  0.00           C  
HETATM   41  C27 UNL     1      13.659  -0.611   1.372  1.00  0.00           C  
HETATM   42  C28 UNL     1      13.835   0.178   0.080  1.00  0.00           C  
HETATM   43  C29 UNL     1      14.506  -1.882   1.261  1.00  0.00           C  
HETATM   44  O13 UNL     1       3.510   0.465  -1.117  1.00  0.00           O  
HETATM   45  C30 UNL     1       2.470   0.937  -1.753  1.00  0.00           C  
HETATM   46  O14 UNL     1       2.397   2.097  -2.326  1.00  0.00           O  
HETATM   47  C31 UNL     1       1.188   0.179  -1.911  1.00  0.00           C  
HETATM   48  C32 UNL     1       0.916  -0.044  -3.415  1.00  0.00           C  
HETATM   49  C33 UNL     1      -0.395  -0.805  -3.466  1.00  0.00           C  
HETATM   50  C34 UNL     1      -1.489   0.096  -3.016  1.00  0.00           C  
HETATM   51  C35 UNL     1      -2.747  -0.272  -2.856  1.00  0.00           C  
HETATM   52  C36 UNL     1      -3.085  -1.645  -2.402  1.00  0.00           C  
HETATM   53  C37 UNL     1      -3.815  -1.652  -1.058  1.00  0.00           C  
HETATM   54  C38 UNL     1      -5.275  -1.622  -1.326  1.00  0.00           C  
HETATM   55  O15 UNL     1      -5.848  -2.659  -1.589  1.00  0.00           O  
HETATM   56  C39 UNL     1      -6.086  -0.372  -1.288  1.00  0.00           C  
HETATM   57  C40 UNL     1      -7.119  -0.316  -0.232  1.00  0.00           C  
HETATM   58  O16 UNL     1      -7.607  -1.581   0.141  1.00  0.00           O  
HETATM   59  C41 UNL     1      -3.337  -2.679  -0.114  1.00  0.00           C  
HETATM   60  N1  UNL     1      -3.903  -4.007  -0.256  1.00  0.00           N  
HETATM   61  C42 UNL     1      -3.927  -4.629  -1.438  1.00  0.00           C  
HETATM   62  C43 UNL     1      -4.483  -5.900  -1.489  1.00  0.00           C  
HETATM   63  C44 UNL     1      -4.994  -6.502  -0.351  1.00  0.00           C  
HETATM   64  N2  UNL     1      -5.569  -7.807  -0.386  1.00  0.00           N  
HETATM   65  N3  UNL     1      -4.956  -5.856   0.820  1.00  0.00           N  
HETATM   66  C45 UNL     1      -4.403  -4.613   0.829  1.00  0.00           C  
HETATM   67  O17 UNL     1      -4.408  -4.077   1.991  1.00  0.00           O  
HETATM   68  O18 UNL     1      -3.257  -2.345   1.196  1.00  0.00           O  
HETATM   69  H1  UNL     1     -13.040   4.619  -0.007  1.00  0.00           H  
HETATM   70  H2  UNL     1     -11.343   5.142   0.166  1.00  0.00           H  
HETATM   71  H3  UNL     1     -12.223   5.598  -1.301  1.00  0.00           H  
HETATM   72  H4  UNL     1     -12.462   2.781  -1.371  1.00  0.00           H  
HETATM   73  H5  UNL     1     -11.163   3.723  -2.182  1.00  0.00           H  
HETATM   74  H6  UNL     1     -10.364   1.829  -0.988  1.00  0.00           H  
HETATM   75  H7  UNL     1      -9.661   3.341  -0.367  1.00  0.00           H  
HETATM   76  H8  UNL     1     -11.382   3.352   1.502  1.00  0.00           H  
HETATM   77  H9  UNL     1     -12.077   1.857   0.892  1.00  0.00           H  
HETATM   78  H10 UNL     1     -10.715   1.305   2.750  1.00  0.00           H  
HETATM   79  H11 UNL     1      -9.853   0.713   1.298  1.00  0.00           H  
HETATM   80  H12 UNL     1      -8.362   1.754   3.086  1.00  0.00           H  
HETATM   81  H13 UNL     1     -10.178   3.341   3.406  1.00  0.00           H  
HETATM   82  H14 UNL     1      -7.917   3.818   0.938  1.00  0.00           H  
HETATM   83  H15 UNL     1      -6.372   2.437  -0.123  1.00  0.00           H  
HETATM   84  H16 UNL     1      -7.630   0.291   1.722  1.00  0.00           H  
HETATM   85  H17 UNL     1      -5.712   0.954   2.644  1.00  0.00           H  
HETATM   86  H18 UNL     1      -4.635   2.176   1.327  1.00  0.00           H  
HETATM   87  H19 UNL     1      -5.739  -1.689   1.496  1.00  0.00           H  
HETATM   88  H20 UNL     1      -6.049  -1.840   3.521  1.00  0.00           H  
HETATM   89  H21 UNL     1      -3.254  -0.239   1.228  1.00  0.00           H  
HETATM   90  H22 UNL     1      -2.952  -0.088   3.489  1.00  0.00           H  
HETATM   91  H23 UNL     1      -3.319  -1.802   3.806  1.00  0.00           H  
HETATM   92  H24 UNL     1      -0.488  -1.393   0.227  1.00  0.00           H  
HETATM   93  H25 UNL     1       2.048  -2.519   4.099  1.00  0.00           H  
HETATM   94  H26 UNL     1       3.361   0.062   1.998  1.00  0.00           H  
HETATM   95  H27 UNL     1       4.470  -1.240   1.433  1.00  0.00           H  
HETATM   96  H28 UNL     1       4.259   1.359   0.544  1.00  0.00           H  
HETATM   97  H29 UNL     1       6.086  -0.163   0.898  1.00  0.00           H  
HETATM   98  H30 UNL     1       5.832  -0.946  -0.684  1.00  0.00           H  
HETATM   99  H31 UNL     1       7.329   2.139  -3.746  1.00  0.00           H  
HETATM  100  H32 UNL     1       6.492   3.432  -2.917  1.00  0.00           H  
HETATM  101  H33 UNL     1       9.237   2.195  -2.264  1.00  0.00           H  
HETATM  102  H34 UNL     1       8.901   3.718  -3.056  1.00  0.00           H  
HETATM  103  H35 UNL     1       9.663   4.289  -0.935  1.00  0.00           H  
HETATM  104  H36 UNL     1       7.907   4.704  -0.971  1.00  0.00           H  
HETATM  105  H37 UNL     1       7.321   2.926   0.481  1.00  0.00           H  
HETATM  106  H38 UNL     1       8.758   3.810   1.156  1.00  0.00           H  
HETATM  107  H39 UNL     1       9.143   1.227  -0.486  1.00  0.00           H  
HETATM  108  H40 UNL     1      10.323   2.231   0.380  1.00  0.00           H  
HETATM  109  H41 UNL     1       8.017   0.836   1.893  1.00  0.00           H  
HETATM  110  H42 UNL     1       9.431   1.730   2.528  1.00  0.00           H  
HETATM  111  H43 UNL     1       9.609  -0.810   0.851  1.00  0.00           H  
HETATM  112  H44 UNL     1       9.803  -0.642   2.664  1.00  0.00           H  
HETATM  113  H45 UNL     1      11.624   0.761   0.616  1.00  0.00           H  
HETATM  114  H46 UNL     1      11.692   0.799   2.438  1.00  0.00           H  
HETATM  115  H47 UNL     1      12.115  -1.596   2.457  1.00  0.00           H  
HETATM  116  H48 UNL     1      11.920  -1.681   0.667  1.00  0.00           H  
HETATM  117  H49 UNL     1      13.978  -0.018   2.235  1.00  0.00           H  
HETATM  118  H50 UNL     1      14.819   0.031  -0.375  1.00  0.00           H  
HETATM  119  H51 UNL     1      13.046  -0.137  -0.647  1.00  0.00           H  
HETATM  120  H52 UNL     1      13.694   1.275   0.263  1.00  0.00           H  
HETATM  121  H53 UNL     1      13.881  -2.792   1.453  1.00  0.00           H  
HETATM  122  H54 UNL     1      14.875  -1.978   0.219  1.00  0.00           H  
HETATM  123  H55 UNL     1      15.314  -1.889   2.023  1.00  0.00           H  
HETATM  124  H56 UNL     1       1.151  -0.774  -1.397  1.00  0.00           H  
HETATM  125  H57 UNL     1       0.325   0.793  -1.569  1.00  0.00           H  
HETATM  126  H58 UNL     1       1.707  -0.709  -3.815  1.00  0.00           H  
HETATM  127  H59 UNL     1       0.818   0.921  -3.908  1.00  0.00           H  
HETATM  128  H60 UNL     1      -0.548  -1.139  -4.516  1.00  0.00           H  
HETATM  129  H61 UNL     1      -0.334  -1.647  -2.750  1.00  0.00           H  
HETATM  130  H62 UNL     1      -1.256   1.159  -2.797  1.00  0.00           H  
HETATM  131  H63 UNL     1      -3.555   0.432  -3.055  1.00  0.00           H  
HETATM  132  H64 UNL     1      -2.193  -2.278  -2.340  1.00  0.00           H  
HETATM  133  H65 UNL     1      -3.780  -2.049  -3.170  1.00  0.00           H  
HETATM  134  H66 UNL     1      -3.586  -0.605  -0.670  1.00  0.00           H  
HETATM  135  H67 UNL     1      -6.512  -0.196  -2.324  1.00  0.00           H  
HETATM  136  H68 UNL     1      -5.326   0.464  -1.207  1.00  0.00           H  
HETATM  137  H69 UNL     1      -8.033   0.159  -0.721  1.00  0.00           H  
HETATM  138  H70 UNL     1      -8.405  -1.538   0.682  1.00  0.00           H  
HETATM  139  H71 UNL     1      -2.251  -2.867  -0.421  1.00  0.00           H  
HETATM  140  H72 UNL     1      -3.538  -4.208  -2.354  1.00  0.00           H  
HETATM  141  H73 UNL     1      -4.543  -6.471  -2.400  1.00  0.00           H  
HETATM  142  H74 UNL     1      -5.216  -8.513   0.269  1.00  0.00           H  
HETATM  143  H75 UNL     1      -6.325  -7.959  -1.090  1.00  0.00           H  
CONECT    1    2   69   70   71
CONECT    2    3   72   73
CONECT    3    4   74   75
CONECT    4    5   76   77
CONECT    5    6   78   79
CONECT    6    7    8   80
CONECT    7   81
CONECT    8    9    9   82
CONECT    9   10   83
CONECT   10   11   57   84
CONECT   11   12   13   85
CONECT   12   86
CONECT   13   14   15   87
CONECT   14   88
CONECT   15   16   68   89
CONECT   16   17   90   91
CONECT   17   18
CONECT   18   19   19   20   21
CONECT   20   92
CONECT   21   22
CONECT   22   23   23   24   25
CONECT   24   93
CONECT   25   26
CONECT   26   27   94   95
CONECT   27   28   44   96
CONECT   28   29   97   98
CONECT   29   30
CONECT   30   31   31   32
CONECT   32   33   99  100
CONECT   33   34  101  102
CONECT   34   35  103  104
CONECT   35   36  105  106
CONECT   36   37  107  108
CONECT   37   38  109  110
CONECT   38   39  111  112
CONECT   39   40  113  114
CONECT   40   41  115  116
CONECT   41   42   43  117
CONECT   42  118  119  120
CONECT   43  121  122  123
CONECT   44   45
CONECT   45   46   46   47
CONECT   47   48  124  125
CONECT   48   49  126  127
CONECT   49   50  128  129
CONECT   50   51   51  130
CONECT   51   52  131
CONECT   52   53  132  133
CONECT   53   54   59  134
CONECT   54   55   55   56
CONECT   56   57  135  136
CONECT   57   58  137
CONECT   58  138
CONECT   59   60   68  139
CONECT   60   61   66
CONECT   61   62   62  140
CONECT   62   63  141
CONECT   63   64   65   65
CONECT   64  142  143
CONECT   65   66
CONECT   66   67   67
END
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SMILES for HMDB0293387 (CDP-DG(i-13:0/PGE2))

CCCCC[C@H](O)C=C[C@H]1[C@H](O)CC(=O)[C@@H]2CC=CCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(O)(=O)OP(O)(=O)OC[C@@H](O[C@H]2N2C=CC(N)=NC2=O)[C@@H](O)[C@H]1O
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INCHI for HMDB0293387 (CDP-DG(i-13:0/PGE2))

InChI=1S/C45H75N3O18P2/c1-4-5-13-19-32(49)23-24-34-36(50)27-37(51)35-20-15-11-12-17-22-41(53)64-33(28-61-40(52)21-16-10-8-6-7-9-14-18-31(2)3)29-62-67(57,58)66-68(59,60)63-30-38(43(55)42(34)54)65-44(35)48-26-25-39(46)47-45(48)56/h11,15,23-26,31-36,38,42-44,49-50,54-55H,4-10,12-14,16-22,27-30H2,1-3H3,(H,57,58)(H,59,60)(H2,46,47,56)/b15-11-,24-23-/t32-,33+,34-,35-,36+,38+,42-,43+,44+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[(1R,9R,15Z,18R,21R,22S,23S,24S,26R)-4,6,21,23,24-Pentahydroxy-26-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-22-[(3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,19-tetraoxo-3,5,7,10,25-pentaoxa-4,6-diphosphabicyclo[16.6.2]hexacos-15-en-9-yl]methyl 11-methyldodecanoic acidHMDB
Chemical FormulaC45H75N3O18P2
Average Molecular Weight1008.046
Monoisotopic Molecular Weight1007.452086583
IUPAC Name[(1R,9R,15Z,18R,21R,22S,23S,24S,26R)-26-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,21,23,24-pentahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,19-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacos-15-en-9-yl]methyl 11-methyldodecanoate
Traditional Name[(1R,9R,15Z,18R,21R,22S,23S,24S,26R)-26-(4-amino-2-oxopyrimidin-1-yl)-4,6,21,23,24-pentahydroxy-22-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,11,19-tetraoxo-3,5,7,10,25-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[16.6.2]hexacos-15-en-9-yl]methyl 11-methyldodecanoate
CAS Registry NumberNot Available
SMILES
CCCCC[C@H](O)C=C[C@H]1[C@H](O)CC(=O)[C@@H]2CC=CCCCC(=O)O[C@H](COC(=O)CCCCCCCCCC(C)C)COP(O)(=O)OP(O)(=O)OC[C@@H](O[C@H]2N2C=CC(N)=NC2=O)[C@@H](O)[C@H]1O
InChI Identifier
InChI=1S/C45H75N3O18P2/c1-4-5-13-19-32(49)23-24-34-36(50)27-37(51)35-20-15-11-12-17-22-41(53)64-33(28-61-40(52)21-16-10-8-6-7-9-14-18-31(2)3)29-62-67(57,58)66-68(59,60)63-30-38(43(55)42(34)54)65-44(35)48-26-25-39(46)47-45(48)56/h11,15,23-26,31-36,38,42-44,49-50,54-55H,4-10,12-14,16-22,27-30H2,1-3H3,(H,57,58)(H,59,60)(H2,46,47,56)/b15-11-,24-23-/t32-,33+,34-,35-,36+,38+,42-,43+,44+/m0/s1
InChI KeyFDTZDJCTGRIIDS-BVOVXBNSSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Glycerophospholipid
  • Organic pyrophosphate
  • Hydroxypyrimidine
  • Fatty acid ester
  • Fatty acyl
  • Pyrimidine
  • Organic phosphoric acid derivative
  • Hydropyrimidine
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Secondary alcohol
  • Lactone
  • Ketone
  • Carboxylic acid ester
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Polyol
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
logP2.49ALOGPS
logP4.78ChemAxon
logS-3.5ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)0.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area320.8 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity248.76 m³·mol⁻¹ChemAxon
Polarizability105.64 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+299.26232859911
AllCCS[M+H-H2O]+299.6432859911
AllCCS[M+Na]+298.75832859911
AllCCS[M+NH4]+298.87632859911
AllCCS[M-H]-298.1932859911
AllCCS[M+Na-2H]-304.99232859911
AllCCS[M+HCOO]-312.40832859911
DeepCCS[M+H]+306.88930932474
DeepCCS[M-H]-304.52530932474
DeepCCS[M-2H]-338.28830932474
DeepCCS[M+Na]+313.21330932474

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, 2022.7.42 minutes32390414
Predicted by Siyang on May 30, 202217.671 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.77 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3536.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid135.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid262.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid182.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid303.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid862.1 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 Acid818.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)510.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1594.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid883.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1639.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid545.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid534.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate249.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA57.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water15.5 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-13:0/PGE2) 10V, Positive-QTOFsplash10-06xx-7500000009-62b54799ee669fef02ed2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-13:0/PGE2) 20V, Positive-QTOFsplash10-05fu-9100000016-723ca738d217908ea06d2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-13:0/PGE2) 40V, Positive-QTOFsplash10-0a4l-9500000200-911edebda96bbd12b9d82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-13:0/PGE2) 10V, Negative-QTOFsplash10-0a4i-9000000003-2be03eb81981f37ad7452021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-13:0/PGE2) 20V, Negative-QTOFsplash10-08g0-4320000229-27c0f38520a3316852582021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(i-13:0/PGE2) 40V, Negative-QTOFsplash10-03dm-4910001302-2909fac8d997b044e1df2021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 References
  1. Hajeyah AA, Griffiths WJ, Wang Y, Finch AJ, O'Donnell VB: The Biosynthesis of Enzymatically Oxidized Lipids. Front Endocrinol (Lausanne). 2020 Nov 19;11:591819. doi: 10.3389/fendo.2020.591819. eCollection 2020. [PubMed:33329396 ]