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Showing metabocard for CDP-DG(PGD2/i-18:0) (HMDB0293909)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 18:01:46 UTC
Update Date2022-11-30 20:08:46 UTC
HMDB IDHMDB0293909
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(PGD2/i-18:0)
DescriptionCDP-DG(PGD2/i-18:0) 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(PGD2/i-18:0), in particular, consists of one chain of one Prostaglandin D2 at the C-1 position and one chain of 16-methylheptadecanoyl 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0293909 (CDP-DG(PGD2/i-18:0))


  Mrv1652309172120022D          

 73 75  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0293909 (CDP-DG(PGD2/i-18:0))

HMDB0293909
     RDKit          3D
CDP-DG(PGD2/i-18:0)
158160  0  0  0  0  0  0  0  0999 V2000
  -12.7466   -0.7745   -1.4381 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8978   -0.6688   -0.1393 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3806    0.5184    0.6143 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7224    0.8557    1.8690 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8448   -0.0382    3.0280 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4008   -1.4335    3.0105 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.5899   -2.0419    4.2970 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.0558   -1.0470    3.3822 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0293909 (CDP-DG(PGD2/i-18:0))


  Mrv1652309172120022D          

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 72 73  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0293909

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC[C@H](O)C=C[C@@H]1[C@H](O)[C@H](O)[C@H]2COP(O)(=O)OP(O)(=O)OC[C@@H](COC(=O)CCC\C=C/C[C@@H]([C@@H](O)CC1=O)[C@@H](O2)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCC(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C50H85N3O18P2/c1-4-5-18-24-37(54)28-29-39-41(55)32-42(56)40-25-20-16-17-21-26-45(57)66-33-38(69-46(58)27-22-15-13-11-9-7-6-8-10-12-14-19-23-36(2)3)34-67-72(62,63)71-73(64,65)68-35-43(48(60)47(39)59)70-49(40)53-31-30-44(51)52-50(53)61/h16,20,28-31,36-40,42-43,47-49,54,56,59-60H,4-15,17-19,21-27,32-35H2,1-3H3,(H,62,63)(H,64,65)(H2,51,52,61)/b20-16-,29-28+/t37-,38+,39-,40-,42-,43+,47-,48?,49+/m0/s1

> <INCHI_KEY>
XKOGDVBZBTZCLN-PNPKVQSISA-N

> <FORMULA>
C50H85N3O18P2

> <MOLECULAR_WEIGHT>
1078.181

> <EXACT_MASS>
1077.530336905

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
158

> <JCHEM_AVERAGE_POLARIZABILITY>
115.16228761472553

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,9R,16Z,19S,20S,23R,24S,25S,27R)-27-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,20,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl 16-methylheptadecanoate

> <ALOGPS_LOGP>
3.82

> <JCHEM_LOGP>
7.10362988336225

> <ALOGPS_LOGS>
-4.39

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.271952704077896

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8709321252782676

> <JCHEM_PKA_STRONGEST_BASIC>
0.34389111225974733

> <JCHEM_POLAR_SURFACE_AREA>
320.8

> <JCHEM_REFRACTIVITY>
271.56

> <JCHEM_ROTATABLE_BOND_COUNT>
24

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.36e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,9R,16Z,19S,20S,23R,24S,25S,27R)-27-(4-amino-2-oxopyrimidin-1-yl)-4,6,20,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl 16-methylheptadecanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0293909 (CDP-DG(PGD2/i-18:0))

HMDB0293909
     RDKit          3D
CDP-DG(PGD2/i-18:0)
158160  0  0  0  0  0  0  0  0999 V2000
  -12.7466   -0.7745   -1.4381 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8978   -0.6688   -0.1393 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3806    0.5184    0.6143 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7224    0.8557    1.8690 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8448   -0.0382    3.0280 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4008   -1.4335    3.0105 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.5899   -2.0419    4.2970 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9534   -1.5668    2.6169 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0558   -1.0470    3.3822 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5803   -0.9952    3.2973 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.8644   -1.9564    2.4960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6911   -2.1683    2.9324 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2043   -2.7181    1.3200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4943   -2.1236    0.0234 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.8047   -3.1467   -0.9218 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4803   -1.2485   -0.6499 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0585   -1.6567   -0.4879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7758   -3.0330   -0.8970 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6023   -3.5708   -0.6168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8699   -3.2290    0.6262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8588   -2.1254    0.4565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6770   -1.3461    1.7523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2485   -1.3574    2.1267 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1142   -2.0034    3.1352 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6654   -0.6657    1.3734 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3515    0.4800    0.6007 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5832    0.9285   -0.1720 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5037   -0.1291   -0.1895 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7282    0.0052    0.4486 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9583    1.1005    1.0225 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7245   -1.1194    0.4475 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9402   -0.7476    1.2092 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7245    0.4138    0.7090 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2600    0.2363   -0.6920 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1419   -0.9655   -0.6931 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7744   -1.2661   -2.0312 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6508   -0.1220   -2.4942 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7710    0.1421   -1.5036 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6482   -1.0835   -1.3326 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7572   -0.8131   -0.3463 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6535    0.3118   -0.7601 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7210    0.4806    0.3107 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6773    1.5794   -0.0228 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4644    1.3553   -1.2560 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4100    0.2143   -1.2832 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4719    0.3355   -0.1887 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8715   -1.1601   -1.3294 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2061    1.4349   -1.5469 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0247    2.1867   -1.3557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1600    1.5748   -2.3593 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.6801    0.3567   -3.0919 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5280    2.7443   -3.5533 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6018    1.2850   -1.5227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9622    2.5073   -0.4419 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.6612    3.2366   -0.1100 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9954    3.6389   -1.1646 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5839    1.9391    1.0214 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7894    2.5690    1.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9210    1.5638    1.3364 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.6334    0.7433    0.2430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7392    0.2201   -0.3547 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.0769    1.0060   -1.5199 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2957    1.0487   -2.6086 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6527    1.8259   -3.7209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8101    2.5733   -3.7472 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1936    3.3686   -4.8614 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5691    2.5007   -2.6282 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2089    1.7527   -1.5776 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9613    1.7321   -0.5725 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8249    0.7558    2.6432 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0933    1.5476    3.5831 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1181    0.4391    3.2551 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.1023    1.2996    2.7086 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.6479   -1.7955   -1.8213 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3329   -0.0960   -2.2102 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.7910   -0.5536   -1.1913 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8419   -0.4995   -0.5214 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9164   -1.6191    0.3739 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.4990    0.3540    0.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3215    1.4403   -0.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6148    1.0614    1.6525 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0465    1.9148    2.1986 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3311    0.5176    3.9070 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.9194   -0.0468    3.4255 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.0794   -2.0560    2.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2699   -2.9864    4.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8324   -2.1134    1.6909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4762   -0.5216    4.2937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3096   -1.3406    4.4074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3598   -3.5001    1.0891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0213   -3.4820    1.5534 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.7057   -1.3389   -1.7577 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1646   -1.3906   -0.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.9698   -1.3878   -2.7821 H   0  0  0  0  0  0  0  0  0  0  0  0
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   10.1064   -0.3879   -3.4560 H   0  0  0  0  0  0  0  0  0  0  0  0
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   14.1893    0.7642    1.2703 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.3116    1.8512    0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.0536    2.5009   -0.1941 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.7414    1.3354   -2.1224 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.0829    2.2836   -1.4617 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.0186    0.3557   -2.2432 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.9751    0.5959    0.7508 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.0458   -0.6093   -0.0983 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.1837    1.1295   -0.4657 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.8670   -1.2618   -1.7294 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.9798   -1.7157   -0.3634 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.5261   -1.7699   -2.0374 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0443    0.6021   -2.2369 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9787    2.1381   -1.8780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2877    2.3390   -4.0734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9126    4.5333   -0.7310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6802    2.9716    2.3883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9835    3.4287    0.6872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8908    2.0505    1.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6586    0.2934    0.2901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3736    0.4919   -2.6620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0137    1.8538   -4.5981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3693    4.3944   -4.7834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3078    2.9285   -5.8010 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1340   -0.0531    2.4135 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8429    0.9944    4.3568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0953    0.7917    4.3428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0195    2.2108    3.0888 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
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  3
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  2  0
 23 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  2  0
 29 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 34 35  1  0
 35 36  1  0
 36 37  1  0
 37 38  1  0
 38 39  1  0
 39 40  1  0
 40 41  1  0
 41 42  1  0
 42 43  1  0
 43 44  1  0
 44 45  1  0
 45 46  1  0
 45 47  1  0
 27 48  1  0
 48 49  1  0
 49 50  1  0
 50 51  2  0
 50 52  1  0
 50 53  1  0
 53 54  1  0
 54 55  2  0
 54 56  1  0
 54 57  1  0
 57 58  1  0
 58 59  1  0
 59 60  1  0
 60 61  1  0
 61 62  1  0
 62 63  1  0
 63 64  2  0
 64 65  1  0
 65 66  1  0
 65 67  2  0
 67 68  1  0
 68 69  2  0
 59 70  1  0
 70 71  1  0
 70 72  1  0
 72 73  1  0
 72 10  1  0
 61 16  1  0
 68 62  1  0
  1 74  1  0
  1 75  1  0
  1 76  1  0
  2 77  1  0
  2 78  1  0
  3 79  1  0
  3 80  1  0
  4 81  1  0
  4 82  1  0
  5 83  1  0
  5 84  1  0
  6 85  1  6
  7 86  1  0
  8 87  1  0
  9 88  1  0
 10 89  1  1
 13 90  1  0
 13 91  1  0
 14 92  1  1
 15 93  1  0
 16 94  1  6
 17 95  1  0
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 18 97  1  0
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 20100  1  0
 21101  1  0
 21102  1  0
 22103  1  0
 22104  1  0
 26105  1  0
 26106  1  0
 27107  1  1
 31108  1  0
 31109  1  0
 32110  1  0
 32111  1  0
 33112  1  0
 33113  1  0
 34114  1  0
 34115  1  0
 35116  1  0
 35117  1  0
 36118  1  0
 36119  1  0
 37120  1  0
 37121  1  0
 38122  1  0
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 40126  1  0
 40127  1  0
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 48143  1  0
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 56146  1  0
 58147  1  0
 58148  1  0
 59149  1  6
 61150  1  1
 63151  1  0
 64152  1  0
 66153  1  0
 66154  1  0
 70155  1  6
 71156  1  0
 72157  1  1
 73158  1  0
M  END
Download

PDB for HMDB0293909 (CDP-DG(PGD2/i-18:0))

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      -8.960  12.378   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -7.501  11.711   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -6.326  12.705   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -4.877  12.185   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.827  13.804   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      -4.603  10.669   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -5.779   9.674   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -7.228  10.195   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.154  10.148   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.388  11.533   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.196  12.578   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.347  13.917   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.089  14.585   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       2.672  14.366   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0       2.256  15.978   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       3.821  15.563   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.967  13.430   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       4.872  12.113   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       5.694  13.576   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       6.578  12.255   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       5.279  10.567   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       5.235   8.985   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.692   7.486   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.859   6.130   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.686   5.069   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.351   4.251   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.633   2.627   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -0.092   3.646   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.617   3.270   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.193   3.414   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.450   4.356   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.891   5.859   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.466   7.359   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -3.447   8.579   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -2.058   7.855   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.763   6.321   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -0.548   7.473   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       0.875   8.123   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       0.682   6.590   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       1.724   9.424   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       3.220   9.574   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       4.743   9.819   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       6.611   9.990   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0       7.619  11.289   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       8.296   9.916   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       9.837   9.423   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      10.167   7.832   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      10.768   6.382   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       9.832   5.160   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0       5.696   5.987   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0       6.542   4.450   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0       6.346   2.887   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0       7.957   3.457   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       9.652   3.147   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      11.302   2.955   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      12.534   4.088   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      14.143   4.101   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      14.922   5.530   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      16.369   4.908   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      17.299   6.186   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      18.645   5.363   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      19.806   6.434   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      21.166   5.615   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      22.405   6.613   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      23.847   5.942   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      25.231   6.737   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      26.641   5.987   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      28.087   6.568   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      27.117   4.424   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0       0.097  11.711   0.000  0.00  0.00           C+0
HETATM   71  O   UNK     0       0.221  10.185   0.000  0.00  0.00           O+0
HETATM   72  C   UNK     0       1.420  10.937   0.000  0.00  0.00           C+0
HETATM   73  O   UNK     0       1.384  12.548   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   34                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   70                                                  
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   50                                                  
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    9   35                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41   72                                                  
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48                                                            
CONECT   50   23   51                                                       
CONECT   51   50   52   53                                                  
CONECT   52   51                                                            
CONECT   53   51   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68   69                                                  
CONECT   68   67                                                            
CONECT   69   67                                                            
CONECT   70   11   71   72                                                  
CONECT   71   70                                                            
CONECT   72   70   40   73                                                  
CONECT   73   72                                                            
MASTER        0    0    0    0    0    0    0    0   73    0  150    0
END
Download

3D PDB for HMDB0293909 (CDP-DG(PGD2/i-18:0))

COMPND    HMDB0293909
HETATM    1  C1  UNL     1     -12.747  -0.774  -1.438  1.00  0.00           C  
HETATM    2  C2  UNL     1     -11.898  -0.669  -0.139  1.00  0.00           C  
HETATM    3  C3  UNL     1     -12.381   0.518   0.614  1.00  0.00           C  
HETATM    4  C4  UNL     1     -11.722   0.856   1.869  1.00  0.00           C  
HETATM    5  C5  UNL     1     -11.845  -0.038   3.028  1.00  0.00           C  
HETATM    6  C6  UNL     1     -11.401  -1.433   3.010  1.00  0.00           C  
HETATM    7  O1  UNL     1     -11.590  -2.042   4.297  1.00  0.00           O  
HETATM    8  C7  UNL     1      -9.953  -1.567   2.617  1.00  0.00           C  
HETATM    9  C8  UNL     1      -9.056  -1.047   3.382  1.00  0.00           C  
HETATM   10  C9  UNL     1      -7.580  -0.995   3.297  1.00  0.00           C  
HETATM   11  C10 UNL     1      -6.864  -1.956   2.496  1.00  0.00           C  
HETATM   12  O2  UNL     1      -5.691  -2.168   2.932  1.00  0.00           O  
HETATM   13  C11 UNL     1      -7.204  -2.718   1.320  1.00  0.00           C  
HETATM   14  C12 UNL     1      -7.494  -2.124   0.023  1.00  0.00           C  
HETATM   15  O3  UNL     1      -7.805  -3.147  -0.922  1.00  0.00           O  
HETATM   16  C13 UNL     1      -6.480  -1.249  -0.650  1.00  0.00           C  
HETATM   17  C14 UNL     1      -5.058  -1.657  -0.488  1.00  0.00           C  
HETATM   18  C15 UNL     1      -4.776  -3.033  -0.897  1.00  0.00           C  
HETATM   19  C16 UNL     1      -3.602  -3.571  -0.617  1.00  0.00           C  
HETATM   20  C17 UNL     1      -2.870  -3.229   0.626  1.00  0.00           C  
HETATM   21  C18 UNL     1      -1.859  -2.125   0.456  1.00  0.00           C  
HETATM   22  C19 UNL     1      -1.677  -1.346   1.752  1.00  0.00           C  
HETATM   23  C20 UNL     1      -0.249  -1.357   2.127  1.00  0.00           C  
HETATM   24  O4  UNL     1       0.114  -2.003   3.135  1.00  0.00           O  
HETATM   25  O5  UNL     1       0.665  -0.666   1.373  1.00  0.00           O  
HETATM   26  C21 UNL     1       0.352   0.480   0.601  1.00  0.00           C  
HETATM   27  C22 UNL     1       1.583   0.928  -0.172  1.00  0.00           C  
HETATM   28  O6  UNL     1       2.504  -0.129  -0.189  1.00  0.00           O  
HETATM   29  C23 UNL     1       3.728   0.005   0.449  1.00  0.00           C  
HETATM   30  O7  UNL     1       3.958   1.100   1.022  1.00  0.00           O  
HETATM   31  C24 UNL     1       4.724  -1.119   0.448  1.00  0.00           C  
HETATM   32  C25 UNL     1       5.940  -0.748   1.209  1.00  0.00           C  
HETATM   33  C26 UNL     1       6.725   0.414   0.709  1.00  0.00           C  
HETATM   34  C27 UNL     1       7.260   0.236  -0.692  1.00  0.00           C  
HETATM   35  C28 UNL     1       8.142  -0.965  -0.693  1.00  0.00           C  
HETATM   36  C29 UNL     1       8.774  -1.266  -2.031  1.00  0.00           C  
HETATM   37  C30 UNL     1       9.651  -0.122  -2.494  1.00  0.00           C  
HETATM   38  C31 UNL     1      10.771   0.142  -1.504  1.00  0.00           C  
HETATM   39  C32 UNL     1      11.648  -1.084  -1.333  1.00  0.00           C  
HETATM   40  C33 UNL     1      12.757  -0.813  -0.346  1.00  0.00           C  
HETATM   41  C34 UNL     1      13.653   0.312  -0.760  1.00  0.00           C  
HETATM   42  C35 UNL     1      14.721   0.481   0.311  1.00  0.00           C  
HETATM   43  C36 UNL     1      15.677   1.579  -0.023  1.00  0.00           C  
HETATM   44  C37 UNL     1      16.464   1.355  -1.256  1.00  0.00           C  
HETATM   45  C38 UNL     1      17.410   0.214  -1.283  1.00  0.00           C  
HETATM   46  C39 UNL     1      18.472   0.336  -0.189  1.00  0.00           C  
HETATM   47  C40 UNL     1      16.872  -1.160  -1.329  1.00  0.00           C  
HETATM   48  C41 UNL     1       1.206   1.435  -1.547  1.00  0.00           C  
HETATM   49  O8  UNL     1       0.025   2.187  -1.356  1.00  0.00           O  
HETATM   50  P1  UNL     1      -1.160   1.575  -2.359  1.00  0.00           P  
HETATM   51  O9  UNL     1      -0.680   0.357  -3.092  1.00  0.00           O  
HETATM   52  O10 UNL     1      -1.528   2.744  -3.553  1.00  0.00           O  
HETATM   53  O11 UNL     1      -2.602   1.285  -1.523  1.00  0.00           O  
HETATM   54  P2  UNL     1      -2.962   2.507  -0.442  1.00  0.00           P  
HETATM   55  O12 UNL     1      -1.661   3.237  -0.110  1.00  0.00           O  
HETATM   56  O13 UNL     1      -3.995   3.639  -1.165  1.00  0.00           O  
HETATM   57  O14 UNL     1      -3.584   1.939   1.021  1.00  0.00           O  
HETATM   58  C42 UNL     1      -4.789   2.569   1.362  1.00  0.00           C  
HETATM   59  C43 UNL     1      -5.921   1.564   1.336  1.00  0.00           C  
HETATM   60  O15 UNL     1      -5.633   0.743   0.243  1.00  0.00           O  
HETATM   61  C44 UNL     1      -6.739   0.220  -0.355  1.00  0.00           C  
HETATM   62  N1  UNL     1      -7.077   1.006  -1.520  1.00  0.00           N  
HETATM   63  C45 UNL     1      -6.296   1.049  -2.609  1.00  0.00           C  
HETATM   64  C46 UNL     1      -6.653   1.826  -3.721  1.00  0.00           C  
HETATM   65  C47 UNL     1      -7.810   2.573  -3.747  1.00  0.00           C  
HETATM   66  N2  UNL     1      -8.194   3.369  -4.861  1.00  0.00           N  
HETATM   67  N3  UNL     1      -8.569   2.501  -2.628  1.00  0.00           N  
HETATM   68  C48 UNL     1      -8.209   1.753  -1.578  1.00  0.00           C  
HETATM   69  O16 UNL     1      -8.961   1.732  -0.573  1.00  0.00           O  
HETATM   70  C49 UNL     1      -5.825   0.756   2.643  1.00  0.00           C  
HETATM   71  O17 UNL     1      -5.093   1.548   3.583  1.00  0.00           O  
HETATM   72  C50 UNL     1      -7.118   0.439   3.255  1.00  0.00           C  
HETATM   73  O18 UNL     1      -8.102   1.300   2.709  1.00  0.00           O  
HETATM   74  H1  UNL     1     -12.648  -1.796  -1.821  1.00  0.00           H  
HETATM   75  H2  UNL     1     -12.333  -0.096  -2.210  1.00  0.00           H  
HETATM   76  H3  UNL     1     -13.791  -0.554  -1.191  1.00  0.00           H  
HETATM   77  H4  UNL     1     -10.842  -0.500  -0.521  1.00  0.00           H  
HETATM   78  H5  UNL     1     -11.916  -1.619   0.374  1.00  0.00           H  
HETATM   79  H6  UNL     1     -13.499   0.354   0.744  1.00  0.00           H  
HETATM   80  H7  UNL     1     -12.322   1.440  -0.071  1.00  0.00           H  
HETATM   81  H8  UNL     1     -10.615   1.061   1.653  1.00  0.00           H  
HETATM   82  H9  UNL     1     -12.046   1.915   2.199  1.00  0.00           H  
HETATM   83  H10 UNL     1     -11.331   0.518   3.907  1.00  0.00           H  
HETATM   84  H11 UNL     1     -12.919  -0.047   3.425  1.00  0.00           H  
HETATM   85  H12 UNL     1     -12.079  -2.056   2.391  1.00  0.00           H  
HETATM   86  H13 UNL     1     -11.270  -2.986   4.137  1.00  0.00           H  
HETATM   87  H14 UNL     1      -9.832  -2.113   1.691  1.00  0.00           H  
HETATM   88  H15 UNL     1      -9.476  -0.522   4.294  1.00  0.00           H  
HETATM   89  H16 UNL     1      -7.310  -1.341   4.407  1.00  0.00           H  
HETATM   90  H17 UNL     1      -6.360  -3.500   1.089  1.00  0.00           H  
HETATM   91  H18 UNL     1      -8.021  -3.482   1.553  1.00  0.00           H  
HETATM   92  H19 UNL     1      -8.432  -1.512   0.012  1.00  0.00           H  
HETATM   93  H20 UNL     1      -7.806  -2.715  -1.808  1.00  0.00           H  
HETATM   94  H21 UNL     1      -6.706  -1.339  -1.758  1.00  0.00           H  
HETATM   95  H22 UNL     1      -4.399  -1.011  -1.146  1.00  0.00           H  
HETATM   96  H23 UNL     1      -4.716  -1.406   0.525  1.00  0.00           H  
HETATM   97  H24 UNL     1      -5.508  -3.611  -1.420  1.00  0.00           H  
HETATM   98  H25 UNL     1      -3.135  -4.295  -1.310  1.00  0.00           H  
HETATM   99  H26 UNL     1      -3.518  -3.033   1.493  1.00  0.00           H  
HETATM  100  H27 UNL     1      -2.279  -4.148   0.917  1.00  0.00           H  
HETATM  101  H28 UNL     1      -2.165  -1.391  -0.319  1.00  0.00           H  
HETATM  102  H29 UNL     1      -0.869  -2.522   0.125  1.00  0.00           H  
HETATM  103  H30 UNL     1      -2.312  -1.789   2.565  1.00  0.00           H  
HETATM  104  H31 UNL     1      -1.992  -0.283   1.665  1.00  0.00           H  
HETATM  105  H32 UNL     1       0.075   1.291   1.289  1.00  0.00           H  
HETATM  106  H33 UNL     1      -0.480   0.306  -0.089  1.00  0.00           H  
HETATM  107  H34 UNL     1       2.028   1.772   0.389  1.00  0.00           H  
HETATM  108  H35 UNL     1       4.934  -1.460  -0.591  1.00  0.00           H  
HETATM  109  H36 UNL     1       4.273  -1.997   0.966  1.00  0.00           H  
HETATM  110  H37 UNL     1       5.583  -0.477   2.254  1.00  0.00           H  
HETATM  111  H38 UNL     1       6.578  -1.647   1.394  1.00  0.00           H  
HETATM  112  H39 UNL     1       7.650   0.460   1.362  1.00  0.00           H  
HETATM  113  H40 UNL     1       6.246   1.401   0.864  1.00  0.00           H  
HETATM  114  H41 UNL     1       6.489   0.207  -1.474  1.00  0.00           H  
HETATM  115  H42 UNL     1       7.890   1.126  -0.910  1.00  0.00           H  
HETATM  116  H43 UNL     1       7.564  -1.857  -0.365  1.00  0.00           H  
HETATM  117  H44 UNL     1       8.937  -0.792   0.085  1.00  0.00           H  
HETATM  118  H45 UNL     1       9.333  -2.211  -2.007  1.00  0.00           H  
HETATM  119  H46 UNL     1       7.970  -1.388  -2.782  1.00  0.00           H  
HETATM  120  H47 UNL     1       9.059   0.805  -2.568  1.00  0.00           H  
HETATM  121  H48 UNL     1      10.106  -0.388  -3.456  1.00  0.00           H  
HETATM  122  H49 UNL     1      10.414   0.502  -0.530  1.00  0.00           H  
HETATM  123  H50 UNL     1      11.406   0.936  -1.948  1.00  0.00           H  
HETATM  124  H51 UNL     1      11.064  -1.951  -0.941  1.00  0.00           H  
HETATM  125  H52 UNL     1      12.084  -1.405  -2.296  1.00  0.00           H  
HETATM  126  H53 UNL     1      13.351  -1.741  -0.205  1.00  0.00           H  
HETATM  127  H54 UNL     1      12.294  -0.566   0.636  1.00  0.00           H  
HETATM  128  H55 UNL     1      13.072   1.274  -0.732  1.00  0.00           H  
HETATM  129  H56 UNL     1      14.075   0.220  -1.758  1.00  0.00           H  
HETATM  130  H57 UNL     1      15.190  -0.485   0.516  1.00  0.00           H  
HETATM  131  H58 UNL     1      14.189   0.764   1.270  1.00  0.00           H  
HETATM  132  H59 UNL     1      16.312   1.851   0.856  1.00  0.00           H  
HETATM  133  H60 UNL     1      15.054   2.501  -0.194  1.00  0.00           H  
HETATM  134  H61 UNL     1      15.741   1.335  -2.122  1.00  0.00           H  
HETATM  135  H62 UNL     1      17.083   2.284  -1.462  1.00  0.00           H  
HETATM  136  H63 UNL     1      18.019   0.356  -2.243  1.00  0.00           H  
HETATM  137  H64 UNL     1      17.975   0.596   0.751  1.00  0.00           H  
HETATM  138  H65 UNL     1      19.046  -0.609  -0.098  1.00  0.00           H  
HETATM  139  H66 UNL     1      19.184   1.129  -0.466  1.00  0.00           H  
HETATM  140  H67 UNL     1      15.867  -1.262  -1.729  1.00  0.00           H  
HETATM  141  H68 UNL     1      16.980  -1.716  -0.363  1.00  0.00           H  
HETATM  142  H69 UNL     1      17.526  -1.770  -2.037  1.00  0.00           H  
HETATM  143  H70 UNL     1       1.044   0.602  -2.237  1.00  0.00           H  
HETATM  144  H71 UNL     1       1.979   2.138  -1.878  1.00  0.00           H  
HETATM  145  H72 UNL     1      -2.288   2.339  -4.073  1.00  0.00           H  
HETATM  146  H73 UNL     1      -3.913   4.533  -0.731  1.00  0.00           H  
HETATM  147  H74 UNL     1      -4.680   2.972   2.388  1.00  0.00           H  
HETATM  148  H75 UNL     1      -4.984   3.429   0.687  1.00  0.00           H  
HETATM  149  H76 UNL     1      -6.891   2.050   1.267  1.00  0.00           H  
HETATM  150  H77 UNL     1      -7.659   0.293   0.290  1.00  0.00           H  
HETATM  151  H78 UNL     1      -5.374   0.492  -2.662  1.00  0.00           H  
HETATM  152  H79 UNL     1      -6.014   1.854  -4.598  1.00  0.00           H  
HETATM  153  H80 UNL     1      -8.369   4.394  -4.783  1.00  0.00           H  
HETATM  154  H81 UNL     1      -8.308   2.929  -5.801  1.00  0.00           H  
HETATM  155  H82 UNL     1      -5.134  -0.053   2.413  1.00  0.00           H  
HETATM  156  H83 UNL     1      -4.843   0.994   4.357  1.00  0.00           H  
HETATM  157  H84 UNL     1      -7.095   0.792   4.343  1.00  0.00           H  
HETATM  158  H85 UNL     1      -8.020   2.211   3.089  1.00  0.00           H  
CONECT    1    2   74   75   76
CONECT    2    3   77   78
CONECT    3    4   79   80
CONECT    4    5   81   82
CONECT    5    6   83   84
CONECT    6    7    8   85
CONECT    7   86
CONECT    8    9    9   87
CONECT    9   10   88
CONECT   10   11   72   89
CONECT   11   12   12   13
CONECT   13   14   90   91
CONECT   14   15   16   92
CONECT   15   93
CONECT   16   17   61   94
CONECT   17   18   95   96
CONECT   18   19   19   97
CONECT   19   20   98
CONECT   20   21   99  100
CONECT   21   22  101  102
CONECT   22   23  103  104
CONECT   23   24   24   25
CONECT   25   26
CONECT   26   27  105  106
CONECT   27   28   48  107
CONECT   28   29
CONECT   29   30   30   31
CONECT   31   32  108  109
CONECT   32   33  110  111
CONECT   33   34  112  113
CONECT   34   35  114  115
CONECT   35   36  116  117
CONECT   36   37  118  119
CONECT   37   38  120  121
CONECT   38   39  122  123
CONECT   39   40  124  125
CONECT   40   41  126  127
CONECT   41   42  128  129
CONECT   42   43  130  131
CONECT   43   44  132  133
CONECT   44   45  134  135
CONECT   45   46   47  136
CONECT   46  137  138  139
CONECT   47  140  141  142
CONECT   48   49  143  144
CONECT   49   50
CONECT   50   51   51   52   53
CONECT   52  145
CONECT   53   54
CONECT   54   55   55   56   57
CONECT   56  146
CONECT   57   58
CONECT   58   59  147  148
CONECT   59   60   70  149
CONECT   60   61
CONECT   61   62  150
CONECT   62   63   68
CONECT   63   64   64  151
CONECT   64   65  152
CONECT   65   66   67   67
CONECT   66  153  154
CONECT   67   68
CONECT   68   69   69
CONECT   70   71   72  155
CONECT   71  156
CONECT   72   73  157
CONECT   73  158
END
Download

SMILES for HMDB0293909 (CDP-DG(PGD2/i-18:0))

CCCCC[C@H](O)C=C[C@@H]1[C@H](O)[C@H](O)[C@H]2COP(O)(=O)OP(O)(=O)OC[C@@H](COC(=O)CCC\C=C/C[C@@H]([C@@H](O)CC1=O)[C@@H](O2)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCC(C)C
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INCHI for HMDB0293909 (CDP-DG(PGD2/i-18:0))

InChI=1S/C50H85N3O18P2/c1-4-5-18-24-37(54)28-29-39-41(55)32-42(56)40-25-20-16-17-21-26-45(57)66-33-38(69-46(58)27-22-15-13-11-9-7-6-8-10-12-14-19-23-36(2)3)34-67-72(62,63)71-73(64,65)68-35-43(48(60)47(39)59)70-49(40)53-31-30-44(51)52-50(53)61/h16,20,28-31,36-40,42-43,47-49,54,56,59-60H,4-15,17-19,21-27,32-35H2,1-3H3,(H,62,63)(H,64,65)(H2,51,52,61)/b20-16-,29-28+/t37-,38+,39-,40-,42-,43+,47-,48?,49+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(1R,9R,16E,19S,20S,23R,24S,27R)-4,6,20,24,25-Pentahydroxy-27-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4,6-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl 16-methylheptadecanoic acidHMDB
Chemical FormulaC50H85N3O18P2
Average Molecular Weight1078.181
Monoisotopic Molecular Weight1077.530336905
IUPAC Name(1R,9R,16Z,19S,20S,23R,24S,25S,27R)-27-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4,6,20,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl 16-methylheptadecanoate
Traditional Name(1R,9R,16Z,19S,20S,23R,24S,25S,27R)-27-(4-amino-2-oxopyrimidin-1-yl)-4,6,20,24,25-pentahydroxy-23-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-4,6,12,22-tetraoxo-3,5,7,11,26-pentaoxa-4lambda5,6lambda5-diphosphabicyclo[17.6.2]heptacos-16-en-9-yl 16-methylheptadecanoate
CAS Registry NumberNot Available
SMILES
CCCCC[C@H](O)C=C[C@@H]1[C@H](O)[C@H](O)[C@H]2COP(O)(=O)OP(O)(=O)OC[C@@H](COC(=O)CCC\C=C/C[C@@H]([C@@H](O)CC1=O)[C@@H](O2)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCC(C)C
InChI Identifier
InChI=1S/C50H85N3O18P2/c1-4-5-18-24-37(54)28-29-39-41(55)32-42(56)40-25-20-16-17-21-26-45(57)66-33-38(69-46(58)27-22-15-13-11-9-7-6-8-10-12-14-19-23-36(2)3)34-67-72(62,63)71-73(64,65)68-35-43(48(60)47(39)59)70-49(40)53-31-30-44(51)52-50(53)61/h16,20,28-31,36-40,42-43,47-49,54,56,59-60H,4-15,17-19,21-27,32-35H2,1-3H3,(H,62,63)(H,64,65)(H2,51,52,61)/b20-16-,29-28+/t37-,38+,39-,40-,42-,43+,47-,48?,49+/m0/s1
InChI KeyXKOGDVBZBTZCLN-PNPKVQSISA-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
  • Cyclic ketone
  • 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
logP3.82ALOGPS
logP7.1ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)0.34ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area320.8 ŲChemAxon
Rotatable Bond Count24ChemAxon
Refractivity271.56 m³·mol⁻¹ChemAxon
Polarizability115.16 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]+312.5132859911
AllCCS[M+H-H2O]+312.99632859911
AllCCS[M+Na]+311.88232859911
AllCCS[M+NH4]+312.02732859911
AllCCS[M-H]-305.54832859911
AllCCS[M+Na-2H]-312.07232859911
AllCCS[M+HCOO]-319.15232859911
DeepCCS[M+H]+281.15130932474
DeepCCS[M-H]-279.29230932474
DeepCCS[M-2H]-313.030932474
DeepCCS[M+Na]+286.81430932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/i-18:0) 10V, Positive-QTOFsplash10-03di-9200000000-14f30ef01227231efeaa2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/i-18:0) 20V, Positive-QTOFsplash10-08mm-9100000002-1f9964533a54826d0add2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/i-18:0) 40V, Positive-QTOFsplash10-0a4l-9300001000-d05ae8b5e53df39fe1ea2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/i-18:0) 10V, Negative-QTOFsplash10-0a6r-9000000002-eebe913e3b97bd27bb872021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/i-18:0) 20V, Negative-QTOFsplash10-06vi-9200000104-86be61c9e4a884bbeee82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(PGD2/i-18:0) 40V, Negative-QTOFsplash10-0400-9500003500-c111b245f5dc90d5e13e2021-10-21Wishart 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 ]