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Showing metabocard for PGP(PGD2/a-25:0) (HMDB0274708)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-13 02:04:17 UTC
Update Date2022-11-30 19:59:53 UTC
HMDB IDHMDB0274708
Secondary Accession NumbersNone
Metabolite Identification
Common NamePGP(PGD2/a-25:0)
DescriptionPGP(PGD2/a-25:0) is an oxidized phosphoglycerophosphate (PGP). Oxidized phosphoglycerophosphates are glycerophospholipids in which a phosphoglycerol moiety occupies a glycerol substitution site and at least one of the fatty acyl chains has undergone oxidation. As all oxidized lipids, oxidized phosphoglycerophosphates 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, phosphoglycerophosphates 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. PGP(PGD2/a-25:0), in particular, consists of one chain of one Prostaglandin D2 at the C-1 position and one chain of 22-methyltetracosanoyl 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 PGPs can be synthesized via three different routes. In one route, the oxidized PGP is synthetized de novo following the same mechanisms as for PGPs 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 PGP backbone, mainely through the action of LOX (PMID: 33329396 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0274708 (PGP(PGD2/a-25:0))


  Mrv1652309132104042D          

 69 69  0  0  1  0            999 V2000
    6.5507   -4.6713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5507   -5.4963    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    7.2652   -6.7338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5507   -7.1463    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.1382   -6.4318    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9632   -7.8608    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8363   -7.5588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6929   -1.3713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.5494   -2.6088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   23.6980   -2.1963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 66 67  1  0  0  0  0
 66 68  1  0  0  0  0
 68 69  1  0  0  0  0
M  END
Download

3D MOL for HMDB0274708 (PGP(PGD2/a-25:0))

HMDB0274708
     RDKit          3D
PGP(PGD2/a-25:0)
163163  0  0  0  0  0  0  0  0999 V2000
    1.9103    1.7692    7.7556 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3136    0.8515    6.6545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1408    1.1478    6.5278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8555    0.3914    5.5110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1612   -1.0149    5.4947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2151   -2.1228    5.5811 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4581   -2.1779    6.7614 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7725   -2.1588    4.4565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342   -2.0642    3.1863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4640   -2.1105    2.1291 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2309   -3.1867    1.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5534   -4.1698    1.2698 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0010   -2.8184   -0.0805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3846   -1.3644    0.0917 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7477   -1.2690    0.3479 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5396   -0.9140    1.2373 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0709    0.3341    1.9035 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1240    1.4195    0.9279 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4857    2.5704    1.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6020    2.9534    2.1296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7826    3.2693    1.5352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7537    3.6271    2.6150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0903    3.9993    2.1391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4834    5.2141    2.1705 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0034    3.0977    1.6345 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3063    3.5297    1.2048 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.6105    4.2458   -1.6120 P   0  0  0  0  0  5  0  0  0  0  0  0
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   -4.9093   -2.6859    0.1848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8242   -3.5538   -0.4250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1578   -4.1863   -1.7188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8788   -4.8881   -2.2240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8090   -3.8240   -2.4660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2581   -2.8681   -3.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3705   -1.7234   -3.7243 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0733   -1.9415   -4.0535 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6342   -0.5364   -4.2056 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1014   -0.4379   -4.4511 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4876    1.0247   -4.6191 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9485    1.1982   -4.7905 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7746    0.7472   -3.6044 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2513    1.0385   -3.8515 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0643    0.6381   -2.6430 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5245    0.9615   -2.8291 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3477    0.5911   -1.6185 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7982    0.9618   -1.8288 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6748    0.6514   -0.6632 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7361   -0.7854   -0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0739    1.1169   -1.0041 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0402    0.8414    0.1310 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8127    1.3135    8.7485 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4216    2.7553    7.7577 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0060    1.8958    7.5463 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8483    1.2432    5.7201 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6579   -0.1331    6.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6501    1.1187    7.5427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1791    2.2822    6.3227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8962    0.9309    5.4299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4710    0.7028    4.4442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9459   -1.2220    6.3146 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0274708 (PGP(PGD2/a-25:0))


  Mrv1652309132104042D          

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 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 27 26  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 27 33  1  0  0  0  0
 33 34  1  6  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  1  0  0  0
 36 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 16 43  1  1  0  0  0
 43 44  1  0  0  0  0
 44 45  2  0  0  0  0
 44 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  1  0  0  0  0
 51 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
 58 59  1  0  0  0  0
 59 60  1  0  0  0  0
 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 64 65  1  0  0  0  0
 65 66  1  0  0  0  0
 66 67  1  0  0  0  0
 66 68  1  0  0  0  0
 68 69  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0274708

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)COP(O)(O)=O)OC(=O)CCCCCCCCCCCCCCCCCCCCC(C)CC)[C@@H](O)CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C51H94O16P2/c1-4-6-25-31-43(52)35-36-47-46(48(54)37-49(47)55)32-27-23-24-28-33-50(56)63-40-45(41-66-69(61,62)65-39-44(53)38-64-68(58,59)60)67-51(57)34-29-22-20-18-16-14-12-10-8-7-9-11-13-15-17-19-21-26-30-42(3)5-2/h23,27,35-36,42-48,52-54H,4-22,24-26,28-34,37-41H2,1-3H3,(H,61,62)(H2,58,59,60)/b27-23-,36-35+/t42?,43-,44-,45+,46+,47+,48-/m0/s1

> <INCHI_KEY>
ZCPVCKOEKNZJNX-MTONHRDCSA-N

> <FORMULA>
C51H94O16P2

> <MOLECULAR_WEIGHT>
1025.245

> <EXACT_MASS>
1024.601710943

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
163

> <JCHEM_AVERAGE_POLARIZABILITY>
116.73167405952174

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2S)-2-hydroxy-3-({hydroxy[(2R)-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}-2-[(22-methyltetracosanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid

> <ALOGPS_LOGP>
6.98

> <JCHEM_LOGP>
11.625741263666667

> <ALOGPS_LOGS>
-6.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.04030616971669

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3552637313459046

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5978824382715837

> <JCHEM_POLAR_SURFACE_AREA>
252.87999999999994

> <JCHEM_REFRACTIVITY>
269.88990000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
48

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.22e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-hydroxy-3-{[hydroxy((2R)-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}-2-[(22-methyltetracosanoyl)oxy]propoxy)phosphoryl]oxy}propoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0274708 (PGP(PGD2/a-25:0))

HMDB0274708
     RDKit          3D
PGP(PGD2/a-25:0)
163163  0  0  0  0  0  0  0  0999 V2000
    1.9103    1.7692    7.7556 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3136    0.8515    6.6545 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1408    1.1478    6.5278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8555    0.3914    5.5110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1612   -1.0149    5.4947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2151   -2.1228    5.5811 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4581   -2.1779    6.7614 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7725   -2.1588    4.4565 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4342   -2.0642    3.1863 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4640   -2.1105    2.1291 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2309   -3.1867    1.1332 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5534   -4.1698    1.2698 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0010   -2.8184   -0.0805 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3846   -1.3644    0.0917 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7477   -1.2690    0.3479 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5396   -0.9140    1.2373 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0709    0.3341    1.9035 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1240    1.4195    0.9279 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4857    2.5704    1.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6020    2.9534    2.1296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7826    3.2693    1.5352 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7537    3.6271    2.6150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0903    3.9993    2.1391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4834    5.2141    2.1705 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0034    3.0977    1.6345 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3063    3.5297    1.2048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0289    2.3328    0.6174 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.3499    2.6998    0.0154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1825    3.7705   -0.8863 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6105    4.2458   -1.6120 P   0  0  0  0  0  5  0  0  0  0  0  0
   -8.7746    5.7474   -1.3705 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9810    3.5157   -0.9866 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5179    4.0611   -3.2984 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8171    2.7632   -3.6513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7465    2.5300   -5.1307 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.4812    2.7899   -5.6434 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1079    1.0872   -5.4663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1531    0.2853   -4.8706 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3634   -1.3540   -5.1224 P   0  0  0  0  0  5  0  0  0  0  0  0
   -8.9097   -1.7130   -6.4661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8120   -2.0667   -5.0168 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2876   -2.0604   -3.8678 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1143    1.2506    1.5409 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4261    0.0800    1.2945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7501    0.0736    0.2082 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3835   -1.1289    2.1298 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4571   -2.1521    1.5138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9093   -2.6859    0.1848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8242   -3.5538   -0.4250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1578   -4.1863   -1.7188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8788   -4.8881   -2.2240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8090   -3.8240   -2.4660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2581   -2.8681   -3.5297 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3705   -1.7234   -3.7243 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0733   -1.9415   -4.0535 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6342   -0.5364   -4.2056 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1014   -0.4379   -4.4511 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4876    1.0247   -4.6191 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9485    1.1982   -4.7905 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7746    0.7472   -3.6044 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2513    1.0385   -3.8515 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0643    0.6381   -2.6430 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5245    0.9615   -2.8291 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3477    0.5911   -1.6185 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7982    0.9618   -1.8288 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6748    0.6514   -0.6632 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7361   -0.7854   -0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0739    1.1169   -1.0041 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0402    0.8414    0.1310 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8127    1.3135    8.7485 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4216    2.7553    7.7577 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0060    1.8958    7.5463 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8483    1.2432    5.7201 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6579   -0.1331    6.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6501    1.1187    7.5427 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1791    2.2822    6.3227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8962    0.9309    5.4299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4710    0.7028    4.4442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9459   -1.2220    6.3146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8595   -1.1681    4.5637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8359   -3.0842    5.5472 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1238   -2.9104    6.8059 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8248   -2.2685    4.6834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6094   -1.9551    2.9417 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4842   -2.3368    2.5701 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8952   -3.4664   -0.2203 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4088   -2.9142   -1.0047 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0854   -0.7722   -0.7968 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2533   -1.6626   -0.4113 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5119   -0.7322    0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4160    0.5513    2.7378 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0707    0.0494    2.3052 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7551    1.2551    0.0420 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6538    3.2663    0.1803 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9135    3.9392    2.5838 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4629    2.2363    2.9227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6978    4.1285    0.8160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1822    2.4174    0.9559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7777    2.7924    3.3533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3635    4.5022    3.2206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1275    4.2434    0.3706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8561    4.0286    1.9995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3795    2.0002   -0.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6831    1.8201   -0.5891 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1277    2.9642    0.7410 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7631    4.1387   -0.8969 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8757    2.5695   -3.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2029    2.0192   -3.1112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4573    3.2014   -5.6460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1713    2.0623   -6.2257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0661    0.9146   -6.5596 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1394    0.8386   -5.1558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8757   -3.0567   -5.0108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0400   -3.0132   -3.8543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3977   -1.5597    2.3148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9611   -0.8642    3.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2966   -2.9543    2.2596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4764   -1.6520    1.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3285   -1.9673   -0.5150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7735   -3.3823    0.4314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8763   -3.0168   -0.4388 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6591   -4.4010    0.3131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6559   -3.5965   -2.4709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8647   -5.0489   -1.4855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5998   -5.5977   -1.4271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1489   -5.3522   -3.1872 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8938   -4.3378   -2.9138 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4374   -3.3144   -1.6007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4702   -3.3960   -4.4976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2563   -2.4743   -3.2120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3636   -1.0208   -2.8281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7480   -1.0212   -4.5434 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5673   -2.3961   -3.1716 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2361   -2.5322   -4.9713 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0986   -0.0214   -5.0563 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3791    0.0914   -3.3187 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4104   -0.9445   -5.3869 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7138   -0.8643   -3.6358 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1916    1.6119   -3.7100 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9758    1.4613   -5.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3128    0.7023   -5.7241 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2281    2.2803   -4.9450 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6582   -0.3462   -3.5094 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4562    1.2141   -2.6643 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5370    0.4249   -4.7512 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4442    2.1041   -4.0744 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9664   -0.4688   -2.5593 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6445    1.0632   -1.7314 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6118    2.0213   -3.1081 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9236    0.3733   -3.6957 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2121   -0.4962   -1.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9006    1.0812   -0.7349 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8631    2.0520   -2.0187 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.1250    0.4578   -2.7582 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3815    1.2219    0.2510 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7107   -1.4992   -1.0986 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7381   -0.9354    0.2410 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9998   -1.0459    0.5463 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.0901    2.1791   -1.2961 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4579    0.5509   -1.8886 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5125    0.7564    1.1063 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.7814    1.6515    0.1355 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.5820   -0.1093   -0.0491 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
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M  END
Download

PDB for HMDB0274708 (PGP(PGD2/a-25:0))

HEADER    PROTEIN                                 13-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-SEP-21         0                                  
HETATM    1  O   UNK     0      12.228  -8.720   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      12.228 -10.260   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.562 -11.030   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      13.562 -12.570   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0      12.228 -13.340   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0      11.458 -12.006   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      12.998 -14.673   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      10.894 -14.110   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      10.894 -11.030   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       9.561 -10.260   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       9.561  -8.720   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       8.021  -8.720   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      11.101  -8.720   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       9.561  -7.180   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      10.894  -6.410   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.894  -4.870   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.561  -4.100   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       8.227  -4.870   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       6.893  -4.100   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       6.893  -2.560   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       5.560  -4.870   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.226  -4.100   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.892  -4.870   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.559  -4.100   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.225  -4.870   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.225  -6.410   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.109  -7.180   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.270  -8.711   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -0.125  -9.742   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -2.776  -9.032   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -3.546  -7.698   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -5.078  -7.537   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -2.516  -6.553   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -2.836  -5.047   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.691  -4.017   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.012  -2.510   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -3.476  -2.034   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -0.867  -1.480   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -1.187   0.027   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -0.043   1.057   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -0.363   2.563   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       0.781   3.594   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      12.228  -4.100   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      13.562  -4.870   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      13.562  -6.410   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      14.895  -4.100   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      16.229  -4.870   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      17.563  -4.100   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      18.896  -4.870   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      20.230  -4.100   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      21.564  -4.870   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      22.897  -4.100   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      24.231  -4.870   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      25.565  -4.100   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      26.899  -4.870   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      28.232  -4.100   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      29.566  -4.870   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      30.900  -4.100   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      32.233  -4.870   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      33.567  -4.100   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      34.901  -4.870   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      36.234  -4.100   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      37.568  -4.870   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      38.902  -4.100   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      40.235  -4.870   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      41.569  -4.100   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      41.569  -2.560   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      42.903  -4.870   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      44.236  -4.100   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5                                                            
CONECT    9    2   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   43                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   33                                                  
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   27   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41                                                            
CONECT   43   16   44                                                       
CONECT   44   43   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
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   68                                                  
CONECT   67   66                                                            
CONECT   68   66   69                                                       
CONECT   69   68                                                            
MASTER        0    0    0    0    0    0    0    0   69    0  138    0
END
Download

3D PDB for HMDB0274708 (PGP(PGD2/a-25:0))

COMPND    HMDB0274708
HETATM    1  C1  UNL     1       1.910   1.769   7.756  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.314   0.851   6.654  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.141   1.148   6.528  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.856   0.391   5.511  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.161  -1.015   5.495  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.215  -2.123   5.581  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.458  -2.178   6.761  1.00  0.00           O  
HETATM    8  C7  UNL     1       0.772  -2.159   4.456  1.00  0.00           C  
HETATM    9  C8  UNL     1       0.434  -2.064   3.186  1.00  0.00           C  
HETATM   10  C9  UNL     1       1.464  -2.110   2.129  1.00  0.00           C  
HETATM   11  C10 UNL     1       1.231  -3.187   1.133  1.00  0.00           C  
HETATM   12  O2  UNL     1       0.553  -4.170   1.270  1.00  0.00           O  
HETATM   13  C11 UNL     1       2.001  -2.818  -0.081  1.00  0.00           C  
HETATM   14  C12 UNL     1       2.385  -1.364   0.092  1.00  0.00           C  
HETATM   15  O3  UNL     1       3.748  -1.269   0.348  1.00  0.00           O  
HETATM   16  C13 UNL     1       1.540  -0.914   1.237  1.00  0.00           C  
HETATM   17  C14 UNL     1       2.071   0.334   1.904  1.00  0.00           C  
HETATM   18  C15 UNL     1       2.124   1.420   0.928  1.00  0.00           C  
HETATM   19  C16 UNL     1       1.486   2.570   1.018  1.00  0.00           C  
HETATM   20  C17 UNL     1       0.602   2.953   2.130  1.00  0.00           C  
HETATM   21  C18 UNL     1      -0.783   3.269   1.535  1.00  0.00           C  
HETATM   22  C19 UNL     1      -1.754   3.627   2.615  1.00  0.00           C  
HETATM   23  C20 UNL     1      -3.090   3.999   2.139  1.00  0.00           C  
HETATM   24  O4  UNL     1      -3.483   5.214   2.171  1.00  0.00           O  
HETATM   25  O5  UNL     1      -4.003   3.098   1.634  1.00  0.00           O  
HETATM   26  C21 UNL     1      -5.306   3.530   1.205  1.00  0.00           C  
HETATM   27  C22 UNL     1      -6.029   2.333   0.617  1.00  0.00           C  
HETATM   28  C23 UNL     1      -7.350   2.700   0.015  1.00  0.00           C  
HETATM   29  O6  UNL     1      -7.182   3.770  -0.886  1.00  0.00           O  
HETATM   30  P1  UNL     1      -8.611   4.246  -1.612  1.00  0.00           P  
HETATM   31  O7  UNL     1      -8.775   5.747  -1.370  1.00  0.00           O  
HETATM   32  O8  UNL     1      -9.981   3.516  -0.987  1.00  0.00           O  
HETATM   33  O9  UNL     1      -8.518   4.061  -3.298  1.00  0.00           O  
HETATM   34  C24 UNL     1      -8.817   2.763  -3.651  1.00  0.00           C  
HETATM   35  C25 UNL     1      -8.746   2.530  -5.131  1.00  0.00           C  
HETATM   36  O10 UNL     1      -7.481   2.790  -5.643  1.00  0.00           O  
HETATM   37  C26 UNL     1      -9.108   1.087  -5.466  1.00  0.00           C  
HETATM   38  O11 UNL     1      -8.153   0.285  -4.871  1.00  0.00           O  
HETATM   39  P2  UNL     1      -8.363  -1.354  -5.122  1.00  0.00           P  
HETATM   40  O12 UNL     1      -8.910  -1.713  -6.466  1.00  0.00           O  
HETATM   41  O13 UNL     1      -6.812  -2.067  -5.017  1.00  0.00           O  
HETATM   42  O14 UNL     1      -9.288  -2.060  -3.868  1.00  0.00           O  
HETATM   43  O15 UNL     1      -6.114   1.251   1.541  1.00  0.00           O  
HETATM   44  C27 UNL     1      -5.426   0.080   1.294  1.00  0.00           C  
HETATM   45  O16 UNL     1      -4.750   0.074   0.208  1.00  0.00           O  
HETATM   46  C28 UNL     1      -5.383  -1.129   2.130  1.00  0.00           C  
HETATM   47  C29 UNL     1      -4.457  -2.152   1.514  1.00  0.00           C  
HETATM   48  C30 UNL     1      -4.909  -2.686   0.185  1.00  0.00           C  
HETATM   49  C31 UNL     1      -3.824  -3.554  -0.425  1.00  0.00           C  
HETATM   50  C32 UNL     1      -4.158  -4.186  -1.719  1.00  0.00           C  
HETATM   51  C33 UNL     1      -2.879  -4.888  -2.224  1.00  0.00           C  
HETATM   52  C34 UNL     1      -1.809  -3.824  -2.466  1.00  0.00           C  
HETATM   53  C35 UNL     1      -2.258  -2.868  -3.530  1.00  0.00           C  
HETATM   54  C36 UNL     1      -1.371  -1.723  -3.724  1.00  0.00           C  
HETATM   55  C37 UNL     1       0.073  -1.941  -4.053  1.00  0.00           C  
HETATM   56  C38 UNL     1       0.634  -0.536  -4.206  1.00  0.00           C  
HETATM   57  C39 UNL     1       2.101  -0.438  -4.451  1.00  0.00           C  
HETATM   58  C40 UNL     1       2.488   1.025  -4.619  1.00  0.00           C  
HETATM   59  C41 UNL     1       3.948   1.198  -4.790  1.00  0.00           C  
HETATM   60  C42 UNL     1       4.775   0.747  -3.604  1.00  0.00           C  
HETATM   61  C43 UNL     1       6.251   1.038  -3.851  1.00  0.00           C  
HETATM   62  C44 UNL     1       7.064   0.638  -2.643  1.00  0.00           C  
HETATM   63  C45 UNL     1       8.525   0.961  -2.829  1.00  0.00           C  
HETATM   64  C46 UNL     1       9.348   0.591  -1.619  1.00  0.00           C  
HETATM   65  C47 UNL     1      10.798   0.962  -1.829  1.00  0.00           C  
HETATM   66  C48 UNL     1      11.675   0.651  -0.663  1.00  0.00           C  
HETATM   67  C49 UNL     1      11.736  -0.785  -0.264  1.00  0.00           C  
HETATM   68  C50 UNL     1      13.074   1.117  -1.004  1.00  0.00           C  
HETATM   69  C51 UNL     1      14.040   0.841   0.131  1.00  0.00           C  
HETATM   70  H1  UNL     1       1.813   1.313   8.748  1.00  0.00           H  
HETATM   71  H2  UNL     1       1.422   2.755   7.758  1.00  0.00           H  
HETATM   72  H3  UNL     1       3.006   1.896   7.546  1.00  0.00           H  
HETATM   73  H4  UNL     1       1.848   1.243   5.720  1.00  0.00           H  
HETATM   74  H5  UNL     1       1.658  -0.133   6.851  1.00  0.00           H  
HETATM   75  H6  UNL     1      -0.650   1.119   7.543  1.00  0.00           H  
HETATM   76  H7  UNL     1      -0.179   2.282   6.323  1.00  0.00           H  
HETATM   77  H8  UNL     1      -1.896   0.931   5.430  1.00  0.00           H  
HETATM   78  H9  UNL     1      -0.471   0.703   4.444  1.00  0.00           H  
HETATM   79  H10 UNL     1      -1.946  -1.222   6.315  1.00  0.00           H  
HETATM   80  H11 UNL     1      -1.860  -1.168   4.564  1.00  0.00           H  
HETATM   81  H12 UNL     1      -0.836  -3.084   5.547  1.00  0.00           H  
HETATM   82  H13 UNL     1       1.124  -2.910   6.806  1.00  0.00           H  
HETATM   83  H14 UNL     1       1.825  -2.269   4.683  1.00  0.00           H  
HETATM   84  H15 UNL     1      -0.609  -1.955   2.942  1.00  0.00           H  
HETATM   85  H16 UNL     1       2.484  -2.337   2.570  1.00  0.00           H  
HETATM   86  H17 UNL     1       2.895  -3.466  -0.220  1.00  0.00           H  
HETATM   87  H18 UNL     1       1.409  -2.914  -1.005  1.00  0.00           H  
HETATM   88  H19 UNL     1       2.085  -0.772  -0.797  1.00  0.00           H  
HETATM   89  H20 UNL     1       4.253  -1.663  -0.411  1.00  0.00           H  
HETATM   90  H21 UNL     1       0.512  -0.732   0.855  1.00  0.00           H  
HETATM   91  H22 UNL     1       1.416   0.551   2.738  1.00  0.00           H  
HETATM   92  H23 UNL     1       3.071   0.049   2.305  1.00  0.00           H  
HETATM   93  H24 UNL     1       2.755   1.255   0.042  1.00  0.00           H  
HETATM   94  H25 UNL     1       1.654   3.266   0.180  1.00  0.00           H  
HETATM   95  H26 UNL     1       0.914   3.939   2.584  1.00  0.00           H  
HETATM   96  H27 UNL     1       0.463   2.236   2.923  1.00  0.00           H  
HETATM   97  H28 UNL     1      -0.698   4.128   0.816  1.00  0.00           H  
HETATM   98  H29 UNL     1      -1.182   2.417   0.956  1.00  0.00           H  
HETATM   99  H30 UNL     1      -1.778   2.792   3.353  1.00  0.00           H  
HETATM  100  H31 UNL     1      -1.364   4.502   3.221  1.00  0.00           H  
HETATM  101  H32 UNL     1      -5.128   4.243   0.371  1.00  0.00           H  
HETATM  102  H33 UNL     1      -5.856   4.029   2.000  1.00  0.00           H  
HETATM  103  H34 UNL     1      -5.379   2.000  -0.230  1.00  0.00           H  
HETATM  104  H35 UNL     1      -7.683   1.820  -0.589  1.00  0.00           H  
HETATM  105  H36 UNL     1      -8.128   2.964   0.741  1.00  0.00           H  
HETATM  106  H37 UNL     1     -10.763   4.139  -0.897  1.00  0.00           H  
HETATM  107  H38 UNL     1      -9.876   2.570  -3.353  1.00  0.00           H  
HETATM  108  H39 UNL     1      -8.203   2.019  -3.111  1.00  0.00           H  
HETATM  109  H40 UNL     1      -9.457   3.201  -5.646  1.00  0.00           H  
HETATM  110  H41 UNL     1      -7.171   2.062  -6.226  1.00  0.00           H  
HETATM  111  H42 UNL     1      -9.066   0.915  -6.560  1.00  0.00           H  
HETATM  112  H43 UNL     1     -10.139   0.839  -5.156  1.00  0.00           H  
HETATM  113  H44 UNL     1      -6.876  -3.057  -5.011  1.00  0.00           H  
HETATM  114  H45 UNL     1      -9.040  -3.013  -3.854  1.00  0.00           H  
HETATM  115  H46 UNL     1      -6.398  -1.560   2.315  1.00  0.00           H  
HETATM  116  H47 UNL     1      -4.961  -0.864   3.108  1.00  0.00           H  
HETATM  117  H48 UNL     1      -4.297  -2.954   2.260  1.00  0.00           H  
HETATM  118  H49 UNL     1      -3.476  -1.652   1.365  1.00  0.00           H  
HETATM  119  H50 UNL     1      -5.328  -1.967  -0.515  1.00  0.00           H  
HETATM  120  H51 UNL     1      -5.774  -3.382   0.431  1.00  0.00           H  
HETATM  121  H52 UNL     1      -2.876  -3.017  -0.439  1.00  0.00           H  
HETATM  122  H53 UNL     1      -3.659  -4.401   0.313  1.00  0.00           H  
HETATM  123  H54 UNL     1      -4.656  -3.597  -2.471  1.00  0.00           H  
HETATM  124  H55 UNL     1      -4.865  -5.049  -1.485  1.00  0.00           H  
HETATM  125  H56 UNL     1      -2.600  -5.598  -1.427  1.00  0.00           H  
HETATM  126  H57 UNL     1      -3.149  -5.352  -3.187  1.00  0.00           H  
HETATM  127  H58 UNL     1      -0.894  -4.338  -2.914  1.00  0.00           H  
HETATM  128  H59 UNL     1      -1.437  -3.314  -1.601  1.00  0.00           H  
HETATM  129  H60 UNL     1      -2.470  -3.396  -4.498  1.00  0.00           H  
HETATM  130  H61 UNL     1      -3.256  -2.474  -3.212  1.00  0.00           H  
HETATM  131  H62 UNL     1      -1.364  -1.021  -2.828  1.00  0.00           H  
HETATM  132  H63 UNL     1      -1.748  -1.021  -4.543  1.00  0.00           H  
HETATM  133  H64 UNL     1       0.567  -2.396  -3.172  1.00  0.00           H  
HETATM  134  H65 UNL     1       0.236  -2.532  -4.971  1.00  0.00           H  
HETATM  135  H66 UNL     1       0.099  -0.021  -5.056  1.00  0.00           H  
HETATM  136  H67 UNL     1       0.379   0.091  -3.319  1.00  0.00           H  
HETATM  137  H68 UNL     1       2.410  -0.944  -5.387  1.00  0.00           H  
HETATM  138  H69 UNL     1       2.714  -0.864  -3.636  1.00  0.00           H  
HETATM  139  H70 UNL     1       2.192   1.612  -3.710  1.00  0.00           H  
HETATM  140  H71 UNL     1       1.976   1.461  -5.511  1.00  0.00           H  
HETATM  141  H72 UNL     1       4.313   0.702  -5.724  1.00  0.00           H  
HETATM  142  H73 UNL     1       4.228   2.280  -4.945  1.00  0.00           H  
HETATM  143  H74 UNL     1       4.658  -0.346  -3.509  1.00  0.00           H  
HETATM  144  H75 UNL     1       4.456   1.214  -2.664  1.00  0.00           H  
HETATM  145  H76 UNL     1       6.537   0.425  -4.751  1.00  0.00           H  
HETATM  146  H77 UNL     1       6.444   2.104  -4.074  1.00  0.00           H  
HETATM  147  H78 UNL     1       6.966  -0.469  -2.559  1.00  0.00           H  
HETATM  148  H79 UNL     1       6.645   1.063  -1.731  1.00  0.00           H  
HETATM  149  H80 UNL     1       8.612   2.021  -3.108  1.00  0.00           H  
HETATM  150  H81 UNL     1       8.924   0.373  -3.696  1.00  0.00           H  
HETATM  151  H82 UNL     1       9.212  -0.496  -1.469  1.00  0.00           H  
HETATM  152  H83 UNL     1       8.901   1.081  -0.735  1.00  0.00           H  
HETATM  153  H84 UNL     1      10.863   2.052  -2.019  1.00  0.00           H  
HETATM  154  H85 UNL     1      11.125   0.458  -2.758  1.00  0.00           H  
HETATM  155  H86 UNL     1      11.381   1.222   0.251  1.00  0.00           H  
HETATM  156  H87 UNL     1      11.711  -1.499  -1.099  1.00  0.00           H  
HETATM  157  H88 UNL     1      12.738  -0.935   0.241  1.00  0.00           H  
HETATM  158  H89 UNL     1      11.000  -1.046   0.546  1.00  0.00           H  
HETATM  159  H90 UNL     1      13.090   2.179  -1.296  1.00  0.00           H  
HETATM  160  H91 UNL     1      13.458   0.551  -1.889  1.00  0.00           H  
HETATM  161  H92 UNL     1      13.512   0.756   1.106  1.00  0.00           H  
HETATM  162  H93 UNL     1      14.781   1.652   0.136  1.00  0.00           H  
HETATM  163  H94 UNL     1      14.582  -0.109  -0.049  1.00  0.00           H  
CONECT    1    2   70   71   72
CONECT    2    3   73   74
CONECT    3    4   75   76
CONECT    4    5   77   78
CONECT    5    6   79   80
CONECT    6    7    8   81
CONECT    7   82
CONECT    8    9    9   83
CONECT    9   10   84
CONECT   10   11   16   85
CONECT   11   12   12   13
CONECT   13   14   86   87
CONECT   14   15   16   88
CONECT   15   89
CONECT   16   17   90
CONECT   17   18   91   92
CONECT   18   19   19   93
CONECT   19   20   94
CONECT   20   21   95   96
CONECT   21   22   97   98
CONECT   22   23   99  100
CONECT   23   24   24   25
CONECT   25   26
CONECT   26   27  101  102
CONECT   27   28   43  103
CONECT   28   29  104  105
CONECT   29   30
CONECT   30   31   31   32   33
CONECT   32  106
CONECT   33   34
CONECT   34   35  107  108
CONECT   35   36   37  109
CONECT   36  110
CONECT   37   38  111  112
CONECT   38   39
CONECT   39   40   40   41   42
CONECT   41  113
CONECT   42  114
CONECT   43   44
CONECT   44   45   45   46
CONECT   46   47  115  116
CONECT   47   48  117  118
CONECT   48   49  119  120
CONECT   49   50  121  122
CONECT   50   51  123  124
CONECT   51   52  125  126
CONECT   52   53  127  128
CONECT   53   54  129  130
CONECT   54   55  131  132
CONECT   55   56  133  134
CONECT   56   57  135  136
CONECT   57   58  137  138
CONECT   58   59  139  140
CONECT   59   60  141  142
CONECT   60   61  143  144
CONECT   61   62  145  146
CONECT   62   63  147  148
CONECT   63   64  149  150
CONECT   64   65  151  152
CONECT   65   66  153  154
CONECT   66   67   68  155
CONECT   67  156  157  158
CONECT   68   69  159  160
CONECT   69  161  162  163
END
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SMILES for HMDB0274708 (PGP(PGD2/a-25:0))

CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)COP(O)(O)=O)OC(=O)CCCCCCCCCCCCCCCCCCCCC(C)CC)[C@@H](O)CC1=O
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INCHI for HMDB0274708 (PGP(PGD2/a-25:0))

InChI=1S/C51H94O16P2/c1-4-6-25-31-43(52)35-36-47-46(48(54)37-49(47)55)32-27-23-24-28-33-50(56)63-40-45(41-66-69(61,62)65-39-44(53)38-64-68(58,59)60)67-51(57)34-29-22-20-18-16-14-12-10-8-7-9-11-13-15-17-19-21-26-30-42(3)5-2/h23,27,35-36,42-48,52-54H,4-22,24-26,28-34,37-41H2,1-3H3,(H,61,62)(H2,58,59,60)/b27-23-,36-35+/t42?,43-,44-,45+,46+,47+,48-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[(2S)-2-Hydroxy-3-({hydroxy[(2R)-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}-2-[(22-methyltetracosanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonateGenerator
Chemical FormulaC51H94O16P2
Average Molecular Weight1025.245
Monoisotopic Molecular Weight1024.601710943
IUPAC Name[(2S)-2-hydroxy-3-({hydroxy[(2R)-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}-2-[(22-methyltetracosanoyl)oxy]propoxy]phosphoryl}oxy)propoxy]phosphonic acid
Traditional Name(2S)-2-hydroxy-3-{[hydroxy((2R)-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}-2-[(22-methyltetracosanoyl)oxy]propoxy)phosphoryl]oxy}propoxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)COP(O)(O)=O)OC(=O)CCCCCCCCCCCCCCCCCCCCC(C)CC)[C@@H](O)CC1=O
InChI Identifier
InChI=1S/C51H94O16P2/c1-4-6-25-31-43(52)35-36-47-46(48(54)37-49(47)55)32-27-23-24-28-33-50(56)63-40-45(41-66-69(61,62)65-39-44(53)38-64-68(58,59)60)67-51(57)34-29-22-20-18-16-14-12-10-8-7-9-11-13-15-17-19-21-26-30-42(3)5-2/h23,27,35-36,42-48,52-54H,4-22,24-26,28-34,37-41H2,1-3H3,(H,61,62)(H2,58,59,60)/b27-23-,36-35+/t42?,43-,44-,45+,46+,47+,48-/m0/s1
InChI KeyZCPVCKOEKNZJNX-MTONHRDCSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effectNot Available
DispositionNot Available
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
logP6.98ALOGPS
logP11.63ChemAxon
logS-6.5ALOGPS
pKa (Strongest Acidic)1.36ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area252.88 ŲChemAxon
Rotatable Bond Count48ChemAxon
Refractivity269.89 m³·mol⁻¹ChemAxon
Polarizability116.73 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+320.60132859911
AllCCS[M+H-H2O]+320.84232859911
AllCCS[M+Na]+320.27432859911
AllCCS[M+NH4]+320.35132859911
AllCCS[M-H]-308.19832859911
AllCCS[M+Na-2H]-314.39132859911
AllCCS[M+HCOO]-321.12832859911
DeepCCS[M+H]+297.78630932474
DeepCCS[M-H]-296.06230932474
DeepCCS[M-2H]-330.09330932474
DeepCCS[M+Na]+304.07830932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD2/a-25:0) 10V, Positive-QTOFsplash10-0a4i-6100000609-8cdec0e64f363d4fd0062021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD2/a-25:0) 20V, Positive-QTOFsplash10-0a4i-4100000239-70bee5cffc3d027341862021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD2/a-25:0) 40V, Positive-QTOFsplash10-05xr-2000090000-a9161d76a0c936920e7a2021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD2/a-25:0) 10V, Negative-QTOFsplash10-00di-9000000001-3726588f4b99acb203132021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD2/a-25:0) 20V, Negative-QTOFsplash10-004i-9003000032-b34520251dd05c23c9152021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PGP(PGD2/a-25:0) 40V, Negative-QTOFsplash10-004i-9032001000-f7df3ff244909eef09a62021-10-19Wishart 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 ]