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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-05-22 15:12:27 UTC

Update Date

2022-03-07 02:49:17 UTC

HMDB ID

HMDB0003034

Secondary Accession Numbers

HMDB03034

Metabolite Identification

Common Name

Prostaglandin D3

Description

Prostaglandin D3 (PGD3) is a prostanoid that has been identified as an inhibitor of human platelet aggregation and as a modulator of autonomic nerve transmission. Prostanoids are a subclass of the lipid mediator group known as eicosanoids. They derive from C-20 polyunsaturated fatty acids, mainly dihomo-gamma-linoleic (20:3n-6), arachidonic (20:4n-6), and eicosapentaenoic (20:5n-3) acids, through the action of cyclooxygenases-1 and -2 (COX-1 and COX-2). The reaction product of COX is the unstable endoperoxide prostaglandin H (PGH) that is further transformed into the individual prostanoids by a series of specific prostanoid synthases. Prostanoids are local-acting mediators formed and inactivated within the same or neighbouring cells prior to their release into circulation as inactive metabolites (15-keto- and 13,14-dihydroketo metabolites). Non-enzymatic peroxidation of arachidonic acid and other fatty acids in vivo can result in prostaglandin-like substances isomeric to the COX-derived prostaglandins that are termed isoprostanes. Prostanoids take part in many physiological and pathophysiological processes in practically every organ, tissue and cell, including the vascular, renal, gastrointestinal and reproductive systems. Their activities are mediated through prostanoid-specific receptors and intracellular signalling pathways, whilst their biosynthesis and action are blocked by nonsteroidal antiinflammatory drugs (NSAID). Isoprostanes are considered to be reliable markers of oxidant stress status and have been linked to inflammation, ischaemia-reperfusion, diabetes, cardiovascular disease, reproductive disorders and diabetes. (PMID: 16986207 , 6252026 , 6952267 , 4019112 , 6945633 Prostaglandins are eicosanoids. The eicosanoids consist of the prostaglandins (PGs), thromboxanes (TXs), leukotrienes (LTs), and lipoxins (LXs). The PGs and TXs are collectively identified as prostanoids. Prostaglandins were originally shown to be synthesized in the prostate gland, thromboxanes from platelets (thrombocytes), and leukotrienes from leukocytes, hence the derivation of their names. All mammalian cells except erythrocytes synthesize eicosanoids. These molecules are extremely potent, able to cause profound physiological effects at very dilute concentrations. All eicosanoids function locally at the site of synthesis, through receptor-mediated G-protein linked signalling pathways.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0003034
     RDKit          3D
Prostaglandin D3
 55 55  0  0  0  0  0  0  0  0999 V2000
   -6.5203    2.8978    1.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3882    1.6958    0.2403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7090    0.5726    0.8748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5986    0.0251    0.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8771    0.4940   -0.7171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4663    0.9588   -0.3631 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7826    1.4053   -1.4755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6641   -0.2049    0.1659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514   -1.0284   -0.6689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2449   -2.1943   -0.2058 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7349   -3.4583   -0.8180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8774   -3.8616   -0.7922 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3879   -4.1743   -1.4788 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5760   -3.5815   -0.7511 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6475   -4.1774    0.4999 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1738   -2.1226   -0.6481 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1281   -1.5095    0.3297 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8977   -0.1427    0.7517 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7747    0.7983    0.5274 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0253    0.5218   -0.1598 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2780    0.7786    0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4995    2.1823    1.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6093    3.1106   -0.0767 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6316    2.7928   -1.2698 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6983    4.4872    0.2035 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5263    3.3008    1.4608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1130    2.5737    2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1459    3.6711    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4646    1.3699    0.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0566    2.0191   -0.7334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1966    0.1647    1.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2032   -0.8257    1.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6908   -0.4394   -1.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3910    1.1675   -1.3859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4767    1.7376    0.4063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0967    2.3056   -1.7434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6108   -0.3373    1.2334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1386   -0.8492   -1.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3430   -2.3233    0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4935   -3.9108   -2.5535 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3308   -5.2717   -1.3239 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5157   -3.7012   -1.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5716   -4.1832    0.8573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2204   -1.7140   -1.6629 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8652   -2.1336    1.2702 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1768   -1.8397    0.2103 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9627    0.1440    1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5359    1.8250    0.8785 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0531    1.2871   -1.0083 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0511   -0.4070   -0.7809 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1139    0.5853   -0.1634 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5062    0.0777    1.4006 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4385    2.2110    1.6662 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6414    2.4496    1.7090 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5642    4.7810    0.6207 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  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
 16 10  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  2 29  1  0
  2 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  1
  7 36  1  0
  8 37  1  0
  9 38  1  0
 10 39  1  1
 13 40  1  0
 13 41  1  0
 14 42  1  6
 15 43  1  0
 16 44  1  6
 17 45  1  0
 17 46  1  0
 18 47  1  0
 19 48  1  0
 20 49  1  0
 20 50  1  0
 21 51  1  0
 21 52  1  0
 22 53  1  0
 22 54  1  0
 25 55  1  0
M  END

 
  Mrv0541 02231219382D          
 
 25 25  0  0  0  0            999 V2000
    8.9877   -7.9454    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.9845   -8.7745    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.2137   -7.6599    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.6826   -7.2746    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1551   -8.9947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6689   -9.1839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6976   -8.3067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9866   -6.8549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.4188   -7.6358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8627   -9.7790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.3810   -8.7676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2411   -7.6358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0965   -9.1701    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9531   -7.2195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8086   -8.7574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0931  -10.0061    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6688   -7.5213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5277   -9.1667    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3774   -7.1015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0930   -7.4033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8051   -6.9836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1000   -8.2255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3566   -9.1636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1064   -8.6638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8283   -9.0803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  2  6  1  1  0  0  0
  3  7  1  0  0  0  0
  3  8  1  6  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  2  0  0  0  0
  9 12  2  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  1  6  0  0  0
 14 17  1  0  0  0  0
 15 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
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 20 22  2  0  0  0  0
  5  7  1  0  0  0  0
 18 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003034

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H30O5/c1-2-3-6-9-15(21)12-13-17-16(18(22)14-19(17)23)10-7-4-5-8-11-20(24)25/h3-4,6-7,12-13,15-18,21-22H,2,5,8-11,14H2,1H3,(H,24,25)/b6-3-,7-4-,13-12+/t15-,16+,17+,18-/m0/s1

> <INCHI_KEY>
ANOICLBSJIMQTA-WXGBOJPQSA-N

> <FORMULA>
C20H30O5

> <MOLECULAR_WEIGHT>
350.4492

> <EXACT_MASS>
350.20932407

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
39.66980751404435

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S,5Z)-3-hydroxyocta-1,5-dien-1-yl]-3-oxocyclopentyl]hept-5-enoic acid

> <ALOGPS_LOGP>
2.88

> <JCHEM_LOGP>
2.8633484803333324

> <ALOGPS_LOGS>
-3.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.980513975690979

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.404553463335216

> <JCHEM_PKA_STRONGEST_BASIC>
-1.635846608129408

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
100.5517

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.48e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
prostaglandin D3

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0003034
     RDKit          3D
Prostaglandin D3
 55 55  0  0  0  0  0  0  0  0999 V2000
   -6.5203    2.8978    1.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3882    1.6958    0.2403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7090    0.5726    0.8748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5986    0.0251    0.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8771    0.4940   -0.7171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4663    0.9588   -0.3631 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7826    1.4053   -1.4755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6641   -0.2049    0.1659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514   -1.0284   -0.6689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2449   -2.1943   -0.2058 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7349   -3.4583   -0.8180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8774   -3.8616   -0.7922 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3879   -4.1743   -1.4788 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5760   -3.5815   -0.7511 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6475   -4.1774    0.4999 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1738   -2.1226   -0.6481 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1281   -1.5095    0.3297 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8977   -0.1427    0.7517 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7747    0.7983    0.5274 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0253    0.5218   -0.1598 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2780    0.7786    0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4995    2.1823    1.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6093    3.1106   -0.0767 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6316    2.7928   -1.2698 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6983    4.4872    0.2035 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5263    3.3008    1.4608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1130    2.5737    2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1459    3.6711    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4646    1.3699    0.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0566    2.0191   -0.7334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1966    0.1647    1.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2032   -0.8257    1.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6908   -0.4394   -1.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4767    1.7376    0.4063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0967    2.3056   -1.7434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6108   -0.3373    1.2334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1386   -0.8492   -1.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3430   -2.3233    0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4935   -3.9108   -2.5535 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3308   -5.2717   -1.3239 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5157   -3.7012   -1.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5716   -4.1832    0.8573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2204   -1.7140   -1.6629 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8652   -2.1336    1.2702 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1768   -1.8397    0.2103 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9627    0.1440    1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5359    1.8250    0.8785 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0531    1.2871   -1.0083 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0511   -0.4070   -0.7809 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1139    0.5853   -0.1634 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5062    0.0777    1.4006 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4385    2.2110    1.6662 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6414    2.4496    1.7090 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5642    4.7810    0.6207 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  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
 16 10  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  2 29  1  0
  2 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  1
  7 36  1  0
  8 37  1  0
  9 38  1  0
 10 39  1  1
 13 40  1  0
 13 41  1  0
 14 42  1  6
 15 43  1  0
 16 44  1  6
 17 45  1  0
 17 46  1  0
 18 47  1  0
 19 48  1  0
 20 49  1  0
 20 50  1  0
 21 51  1  0
 21 52  1  0
 22 53  1  0
 22 54  1  0
 25 55  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      16.777 -14.831   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      16.771 -16.379   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.332 -14.298   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.074 -13.579   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.223 -16.790   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.049 -17.143   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.369 -15.506   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      14.908 -12.796   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      19.448 -14.253   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      14.677 -18.254   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      19.378 -16.366   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.983 -14.253   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      20.713 -17.118   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      22.312 -13.476   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.043 -16.347   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      20.707 -18.678   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      23.648 -14.040   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      23.385 -17.111   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      24.971 -13.256   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      26.307 -13.819   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      27.636 -13.036   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      26.320 -15.354   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      24.932 -17.105   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      26.332 -16.172   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      27.679 -16.950   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10    7                                                  
CONECT    6    2   11                                                       
CONECT    7    3    5                                                       
CONECT    8    3                                                            
CONECT    9    4   12                                                       
CONECT   10    5                                                            
CONECT   11    6   13                                                       
CONECT   12    9   14                                                       
CONECT   13   11   15   16                                                  
CONECT   14   12   17                                                       
CONECT   15   13   18                                                       
CONECT   16   13                                                            
CONECT   17   14   19                                                       
CONECT   18   15   23                                                       
CONECT   19   17   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   18   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   50    0
END

COMPND    HMDB0003034
HETATM    1  C1  UNL     1      -6.520   2.898   1.187  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.388   1.696   0.240  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.709   0.573   0.875  1.00  0.00           C  
HETATM    4  C4  UNL     1      -4.599   0.025   0.469  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.877   0.494  -0.717  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.466   0.959  -0.363  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.783   1.405  -1.475  1.00  0.00           O  
HETATM    8  C7  UNL     1      -1.664  -0.205   0.166  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.051  -1.028  -0.669  1.00  0.00           C  
HETATM   10  C9  UNL     1      -0.245  -2.194  -0.206  1.00  0.00           C  
HETATM   11  C10 UNL     1      -0.735  -3.458  -0.818  1.00  0.00           C  
HETATM   12  O2  UNL     1      -1.877  -3.862  -0.792  1.00  0.00           O  
HETATM   13  C11 UNL     1       0.388  -4.174  -1.479  1.00  0.00           C  
HETATM   14  C12 UNL     1       1.576  -3.582  -0.751  1.00  0.00           C  
HETATM   15  O3  UNL     1       1.647  -4.177   0.500  1.00  0.00           O  
HETATM   16  C13 UNL     1       1.174  -2.123  -0.648  1.00  0.00           C  
HETATM   17  C14 UNL     1       2.128  -1.509   0.330  1.00  0.00           C  
HETATM   18  C15 UNL     1       1.898  -0.143   0.752  1.00  0.00           C  
HETATM   19  C16 UNL     1       2.775   0.798   0.527  1.00  0.00           C  
HETATM   20  C17 UNL     1       4.025   0.522  -0.160  1.00  0.00           C  
HETATM   21  C18 UNL     1       5.278   0.779   0.582  1.00  0.00           C  
HETATM   22  C19 UNL     1       5.499   2.182   1.046  1.00  0.00           C  
HETATM   23  C20 UNL     1       5.609   3.111  -0.077  1.00  0.00           C  
HETATM   24  O4  UNL     1       5.632   2.793  -1.270  1.00  0.00           O  
HETATM   25  O5  UNL     1       5.698   4.487   0.203  1.00  0.00           O  
HETATM   26  H1  UNL     1      -5.526   3.301   1.461  1.00  0.00           H  
HETATM   27  H2  UNL     1      -7.113   2.574   2.047  1.00  0.00           H  
HETATM   28  H3  UNL     1      -7.146   3.671   0.656  1.00  0.00           H  
HETATM   29  H4  UNL     1      -7.465   1.370   0.095  1.00  0.00           H  
HETATM   30  H5  UNL     1      -6.057   2.019  -0.733  1.00  0.00           H  
HETATM   31  H6  UNL     1      -6.197   0.165   1.779  1.00  0.00           H  
HETATM   32  H7  UNL     1      -4.203  -0.826   1.057  1.00  0.00           H  
HETATM   33  H8  UNL     1      -3.691  -0.439  -1.338  1.00  0.00           H  
HETATM   34  H9  UNL     1      -4.391   1.168  -1.386  1.00  0.00           H  
HETATM   35  H10 UNL     1      -2.477   1.738   0.406  1.00  0.00           H  
HETATM   36  H11 UNL     1      -2.097   2.306  -1.743  1.00  0.00           H  
HETATM   37  H12 UNL     1      -1.611  -0.337   1.233  1.00  0.00           H  
HETATM   38  H13 UNL     1      -1.139  -0.849  -1.729  1.00  0.00           H  
HETATM   39  H14 UNL     1      -0.343  -2.323   0.907  1.00  0.00           H  
HETATM   40  H15 UNL     1       0.494  -3.911  -2.553  1.00  0.00           H  
HETATM   41  H16 UNL     1       0.331  -5.272  -1.324  1.00  0.00           H  
HETATM   42  H17 UNL     1       2.516  -3.701  -1.328  1.00  0.00           H  
HETATM   43  H18 UNL     1       2.572  -4.183   0.857  1.00  0.00           H  
HETATM   44  H19 UNL     1       1.220  -1.714  -1.663  1.00  0.00           H  
HETATM   45  H20 UNL     1       1.865  -2.134   1.270  1.00  0.00           H  
HETATM   46  H21 UNL     1       3.177  -1.840   0.210  1.00  0.00           H  
HETATM   47  H22 UNL     1       0.963   0.144   1.287  1.00  0.00           H  
HETATM   48  H23 UNL     1       2.536   1.825   0.879  1.00  0.00           H  
HETATM   49  H24 UNL     1       4.053   1.287  -1.008  1.00  0.00           H  
HETATM   50  H25 UNL     1       4.051  -0.407  -0.781  1.00  0.00           H  
HETATM   51  H26 UNL     1       6.114   0.585  -0.163  1.00  0.00           H  
HETATM   52  H27 UNL     1       5.506   0.078   1.401  1.00  0.00           H  
HETATM   53  H28 UNL     1       6.439   2.211   1.666  1.00  0.00           H  
HETATM   54  H29 UNL     1       4.641   2.450   1.709  1.00  0.00           H  
HETATM   55  H30 UNL     1       6.564   4.781   0.621  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3   29   30
CONECT    3    4    4   31
CONECT    4    5   32
CONECT    5    6   33   34
CONECT    6    7    8   35
CONECT    7   36
CONECT    8    9    9   37
CONECT    9   10   38
CONECT   10   11   16   39
CONECT   11   12   12   13
CONECT   13   14   40   41
CONECT   14   15   16   42
CONECT   15   43
CONECT   16   17   44
CONECT   17   18   45   46
CONECT   18   19   19   47
CONECT   19   20   48
CONECT   20   21   49   50
CONECT   21   22   51   52
CONECT   22   23   53   54
CONECT   23   24   24   25
CONECT   25   55
END

HMDB0003034
     RDKit          3D
Prostaglandin D3
 55 55  0  0  0  0  0  0  0  0999 V2000
   -6.5203    2.8978    1.1870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3882    1.6958    0.2403 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7090    0.5726    0.8748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5986    0.0251    0.4694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8771    0.4940   -0.7171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4663    0.9588   -0.3631 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7826    1.4053   -1.4755 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6641   -0.2049    0.1659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0514   -1.0284   -0.6689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2449   -2.1943   -0.2058 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7349   -3.4583   -0.8180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8774   -3.8616   -0.7922 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3879   -4.1743   -1.4788 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5760   -3.5815   -0.7511 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6475   -4.1774    0.4999 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1738   -2.1226   -0.6481 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1281   -1.5095    0.3297 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8977   -0.1427    0.7517 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7747    0.7983    0.5274 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0253    0.5218   -0.1598 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2780    0.7786    0.5824 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4995    2.1823    1.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6093    3.1106   -0.0767 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6316    2.7928   -1.2698 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6983    4.4872    0.2035 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5263    3.3008    1.4608 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1130    2.5737    2.0471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1459    3.6711    0.6563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4646    1.3699    0.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0566    2.0191   -0.7334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1966    0.1647    1.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2032   -0.8257    1.0573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6908   -0.4394   -1.3377 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3910    1.1675   -1.3859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4767    1.7376    0.4063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0967    2.3056   -1.7434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6108   -0.3373    1.2334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1386   -0.8492   -1.7289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3430   -2.3233    0.9065 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4935   -3.9108   -2.5535 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3308   -5.2717   -1.3239 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5157   -3.7012   -1.3284 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5716   -4.1832    0.8573 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2204   -1.7140   -1.6629 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8652   -2.1336    1.2702 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1768   -1.8397    0.2103 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9627    0.1440    1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5359    1.8250    0.8785 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0531    1.2871   -1.0083 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0511   -0.4070   -0.7809 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1139    0.5853   -0.1634 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5062    0.0777    1.4006 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4385    2.2110    1.6662 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6414    2.4496    1.7090 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5642    4.7810    0.6207 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  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
 16 10  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  2 29  1  0
  2 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  1
  7 36  1  0
  8 37  1  0
  9 38  1  0
 10 39  1  1
 13 40  1  0
 13 41  1  0
 14 42  1  6
 15 43  1  0
 16 44  1  6
 17 45  1  0
 17 46  1  0
 18 47  1  0
 19 48  1  0
 20 49  1  0
 20 50  1  0
 21 51  1  0
 21 52  1  0
 22 53  1  0
 22 54  1  0
 25 55  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(5Z)-7-[(1R,2R,5S)-5-Hydroxy-2-[(1E,3S,5Z)-3-hydroxyocta-1,5-dien-1-yl]-3-oxocyclopentyl]hept-5-enoic acid	ChEBI
(5Z,13E,15S,17Z)-9alpha,15-Dihydroxy-11-oxoprosta-5,13,17-trien-1-Oic acid	ChEBI
9S,15S-Dihydroxy-11-oxo-5Z,13E,17Z-prostatrienoic acid	ChEBI
(5Z)-7-[(1R,2R,5S)-5-Hydroxy-2-[(1E,3S,5Z)-3-hydroxyocta-1,5-dien-1-yl]-3-oxocyclopentyl]hept-5-enoate	Generator
(5Z,13E,15S,17Z)-9a,15-Dihydroxy-11-oxoprosta-5,13,17-trien-1-Oate	Generator
(5Z,13E,15S,17Z)-9a,15-Dihydroxy-11-oxoprosta-5,13,17-trien-1-Oic acid	Generator
(5Z,13E,15S,17Z)-9alpha,15-Dihydroxy-11-oxoprosta-5,13,17-trien-1-Oate	Generator
(5Z,13E,15S,17Z)-9Α,15-dihydroxy-11-oxoprosta-5,13,17-trien-1-Oate	Generator
(5Z,13E,15S,17Z)-9Α,15-dihydroxy-11-oxoprosta-5,13,17-trien-1-Oic acid	Generator
9S,15S-Dihydroxy-11-oxo-5Z,13E,17Z-prostatrienoate	Generator
PGD3	HMDB
Prostaglandin D3	MeSH

Chemical Formula

C₂₀H₃₀O₅

Average Molecular Weight

350.4492

Monoisotopic Molecular Weight

350.20932407

IUPAC Name

(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S,5Z)-3-hydroxyocta-1,5-dien-1-yl]-3-oxocyclopentyl]hept-5-enoic acid

Traditional Name

prostaglandin D3

CAS Registry Number

71902-47-1

SMILES

CC\C=C/C[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(O)=O)[C@@H](O)CC1=O

InChI Identifier

InChI=1S/C20H30O5/c1-2-3-6-9-15(21)12-13-17-16(18(22)14-19(17)23)10-7-4-5-8-11-20(24)25/h3-4,6-7,12-13,15-18,21-22H,2,5,8-11,14H2,1H3,(H,24,25)/b6-3-,7-4-,13-12+/t15-,16+,17+,18-/m0/s1

InChI Key

ANOICLBSJIMQTA-WXGBOJPQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Eicosanoids

Direct Parent

Prostaglandins and related compounds

Alternative Parents

Substituents

Prostaglandin skeleton
Long-chain fatty acid
Hydroxy fatty acid
Cyclopentanol
Fatty acid
Unsaturated fatty acid
Cyclic alcohol
Ketone
Cyclic ketone
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

prostaglandins D (CHEBI:34939 )
Prostaglandins (C13802 )
Prostaglandins (LMFA03010142 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 20671299)

Cellular substructure

Extracellular (HMDB: HMDB0003034)
Membrane (HMDB: HMDB0003034)

Source

Exogenous

Exogenous (HMDB: HMDB0003034)

Food

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Endogenous

Endogenous (HMDB: HMDB0003034)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.085 g/L	ALOGPS
logP	2.88	ALOGPS
logP	2.86	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	4.4	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	100.55 m³·mol⁻¹	ChemAxon
Polarizability	39.67 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	187.502	31661259
DarkChem	[M-H]-	183.431	31661259
DeepCCS	[M+H]+	194.114	30932474
DeepCCS	[M-H]-	191.718	30932474
DeepCCS	[M-2H]-	224.654	30932474
DeepCCS	[M+Na]+	200.026	30932474
AllCCS	[M+H]+	191.7	32859911
AllCCS	[M+H-H2O]+	189.0	32859911
AllCCS	[M+NH4]+	194.3	32859911
AllCCS	[M+Na]+	195.0	32859911
AllCCS	[M-H]-	189.9	32859911
AllCCS	[M+Na-2H]-	191.3	32859911
AllCCS	[M+HCOO]-	192.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Prostaglandin D3	CC\C=C/C[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(O)=O)[C@@H](O)CC1=O	4478.1	Standard polar	33892256
Prostaglandin D3	CC\C=C/C[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(O)=O)[C@@H](O)CC1=O	2671.7	Standard non polar	33892256
Prostaglandin D3	CC\C=C/C[C@H](O)\C=C\[C@@H]1[C@@H](C\C=C/CCCC(O)=O)[C@@H](O)CC1=O	2904.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Prostaglandin D3,1TMS,isomer #1	CC/C=C\C[C@@H](/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C	2904.2	Semi standard non polar	33892256
Prostaglandin D3,1TMS,isomer #2	CC/C=C\C[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C	2804.1	Semi standard non polar	33892256
Prostaglandin D3,1TMS,isomer #3	CC/C=C\C[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O	2811.3	Semi standard non polar	33892256
Prostaglandin D3,1TMS,isomer #4	CC/C=C\C[C@H](O)/C=C/C1=C(O[Si](C)(C)C)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O	2879.5	Semi standard non polar	33892256
Prostaglandin D3,1TMS,isomer #5	CC/C=C\C[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O	2759.9	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #1	CC/C=C\C[C@@H](/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C	2772.7	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #2	CC/C=C\C[C@@H](/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2812.2	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #3	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C	2955.0	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #4	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C	2796.4	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #5	CC/C=C\C[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C	2756.2	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #6	CC/C=C\C[C@H](O)/C=C/C1=C(O[Si](C)(C)C)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C	2861.4	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #7	CC/C=C\C[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C	2744.9	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #8	CC/C=C\C[C@H](O)/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O	2847.7	Semi standard non polar	33892256
Prostaglandin D3,2TMS,isomer #9	CC/C=C\C[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O	2778.0	Semi standard non polar	33892256
Prostaglandin D3,3TMS,isomer #1	CC/C=C\C[C@@H](/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2741.3	Semi standard non polar	33892256
Prostaglandin D3,3TMS,isomer #2	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C	2867.1	Semi standard non polar	33892256
Prostaglandin D3,3TMS,isomer #3	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C	2789.1	Semi standard non polar	33892256
Prostaglandin D3,3TMS,isomer #4	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2894.8	Semi standard non polar	33892256
Prostaglandin D3,3TMS,isomer #5	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2767.8	Semi standard non polar	33892256
Prostaglandin D3,3TMS,isomer #6	CC/C=C\C[C@H](O)/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C	2813.8	Semi standard non polar	33892256
Prostaglandin D3,3TMS,isomer #7	CC/C=C\C[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C	2749.1	Semi standard non polar	33892256
Prostaglandin D3,4TMS,isomer #1	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2836.6	Semi standard non polar	33892256
Prostaglandin D3,4TMS,isomer #1	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2811.6	Standard non polar	33892256
Prostaglandin D3,4TMS,isomer #1	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2896.3	Standard polar	33892256
Prostaglandin D3,4TMS,isomer #2	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2796.3	Semi standard non polar	33892256
Prostaglandin D3,4TMS,isomer #2	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2670.2	Standard non polar	33892256
Prostaglandin D3,4TMS,isomer #2	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2904.3	Standard polar	33892256
Prostaglandin D3,1TBDMS,isomer #1	CC/C=C\C[C@@H](/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C(C)(C)C	3134.0	Semi standard non polar	33892256
Prostaglandin D3,1TBDMS,isomer #2	CC/C=C\C[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C	3055.0	Semi standard non polar	33892256
Prostaglandin D3,1TBDMS,isomer #3	CC/C=C\C[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O	3015.0	Semi standard non polar	33892256
Prostaglandin D3,1TBDMS,isomer #4	CC/C=C\C[C@H](O)/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O	3108.0	Semi standard non polar	33892256
Prostaglandin D3,1TBDMS,isomer #5	CC/C=C\C[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O	3011.0	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #1	CC/C=C\C[C@@H](/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C(C)(C)C	3246.2	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #2	CC/C=C\C[C@@H](/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3296.4	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #3	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C(C)(C)C	3376.6	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #4	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C(C)(C)C	3276.8	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #5	CC/C=C\C[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C	3224.1	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #6	CC/C=C\C[C@H](O)/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C	3321.5	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #7	CC/C=C\C[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C	3241.4	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #8	CC/C=C\C[C@H](O)/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O	3280.5	Semi standard non polar	33892256
Prostaglandin D3,2TBDMS,isomer #9	CC/C=C\C[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O	3241.6	Semi standard non polar	33892256
Prostaglandin D3,3TBDMS,isomer #1	CC/C=C\C[C@@H](/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3458.7	Semi standard non polar	33892256
Prostaglandin D3,3TBDMS,isomer #2	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C(C)(C)C	3506.4	Semi standard non polar	33892256
Prostaglandin D3,3TBDMS,isomer #3	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C(C)(C)C	3502.8	Semi standard non polar	33892256
Prostaglandin D3,3TBDMS,isomer #4	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3563.4	Semi standard non polar	33892256
Prostaglandin D3,3TBDMS,isomer #5	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3503.1	Semi standard non polar	33892256
Prostaglandin D3,3TBDMS,isomer #6	CC/C=C\C[C@H](O)/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C	3496.2	Semi standard non polar	33892256
Prostaglandin D3,3TBDMS,isomer #7	CC/C=C\C[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C	3473.1	Semi standard non polar	33892256
Prostaglandin D3,4TBDMS,isomer #1	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3667.8	Semi standard non polar	33892256
Prostaglandin D3,4TBDMS,isomer #1	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3438.2	Standard non polar	33892256
Prostaglandin D3,4TBDMS,isomer #1	CC/C=C\C[C@@H](/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3150.6	Standard polar	33892256
Prostaglandin D3,4TBDMS,isomer #2	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3689.0	Semi standard non polar	33892256
Prostaglandin D3,4TBDMS,isomer #2	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3214.6	Standard non polar	33892256
Prostaglandin D3,4TBDMS,isomer #2	CC/C=C\C[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3155.3	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Prostaglandin D3 GC-MS (Non-derivatized) - 70eV, Positive	splash10-05po-8395000000-44ba79a27b1cb029e065	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Prostaglandin D3 GC-MS (3 TMS) - 70eV, Positive	splash10-0udi-3620690000-cee4d57fecd9b1501065	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Prostaglandin D3 GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 10V, Positive-QTOF	splash10-00lr-0019000000-556c5941c1bd947aa13d	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 20V, Positive-QTOF	splash10-0159-3096000000-7308f804ecfd913b1984	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 40V, Positive-QTOF	splash10-014r-9310000000-135a6bbfabaf1b739b8a	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 10V, Negative-QTOF	splash10-000t-0009000000-50f3213aa3eff0d0faf7	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 20V, Negative-QTOF	splash10-001j-2149000000-89d63bd18af619a97e66	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 40V, Negative-QTOF	splash10-0a4i-9531000000-1f37f093b3d2f8ec45af	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 10V, Negative-QTOF	splash10-000t-0009000000-669e3ea846c980353beb	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 20V, Negative-QTOF	splash10-06rt-0059000000-3be047d22831afb5d0f0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 40V, Negative-QTOF	splash10-052p-9441000000-6a5fd85e6df4f33930ae	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 10V, Positive-QTOF	splash10-014i-0019000000-928cd476df97ec2d1eb4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 20V, Positive-QTOF	splash10-014i-4194000000-7014986c36784cd7e024	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D3 40V, Positive-QTOF	splash10-05mo-9310000000-3fcdcc5aa45a25f6dab0	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.000123 +/- 0.000015 uM	Adult (>18 years old)	Both	Normal	20671299	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023097

KNApSAcK ID

Not Available

Chemspider ID

4445434

KEGG Compound ID

C13802

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

2560

PubChem Compound

5282260

PDB ID

Not Available

ChEBI ID

34939

Food Biomarker Ontology

Not Available

VMH ID

HC02210

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Tsikas D, Schwedhelm E, Suchy MT, Niemann J, Gutzki FM, Erpenbeck VJ, Hohlfeld JM, Surdacki A, Frolich JC: Divergence in urinary 8-iso-PGF(2alpha) (iPF(2alpha)-III, 15-F(2t)-IsoP) levels from gas chromatography-tandem mass spectrometry quantification after thin-layer chromatography and immunoaffinity column chromatography reveals heterogeneity of 8-iso-PGF(2alpha). Possible methodological, mechanistic and clinical implications. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Sep 5;794(2):237-55. [PubMed:12954376 ]
Masoodi M, Nicolaou A: Lipidomic analysis of twenty-seven prostanoids and isoprostanes by liquid chromatography/electrospray tandem mass spectrometry. Rapid Commun Mass Spectrom. 2006;20(20):3023-9. [PubMed:16986207 ]
Hemker DP, Aiken JW: Effects of prostaglandin D3 on nerve transmission in nictitating membrane of cats. Eur J Pharmacol. 1980 Oct 3;67(1):155-8. [PubMed:6252026 ]
Hemker DP, Aiken JW: Effects of prostaglandins on autonomic function in vivo, with special emphasis on PGD2 and PGD3. Prog Lipid Res. 1981;20:511-4. [PubMed:6952267 ]
Kulkarni PS, Srinivasan BD: Prostaglandins E3 and D3 lower intraocular pressure. Invest Ophthalmol Vis Sci. 1985 Aug;26(8):1178-82. [PubMed:4019112 ]
Wendling MG, DuCharme DW: Cardiovascular effects of prostaglandin D3 and D2 in anesthetized dogs. Prostaglandins. 1981 Aug;22(2):235-43. [PubMed:6945633 ]

Showing metabocard for Prostaglandin D3 (HMDB0003034)

MOL for HMDB0003034 (Prostaglandin D3)

3D MOL for HMDB0003034 (Prostaglandin D3)

3D SDF for HMDB0003034 (Prostaglandin D3)

3D-SDF for HMDB0003034 (Prostaglandin D3)

PDB for HMDB0003034 (Prostaglandin D3)

3D PDB for HMDB0003034 (Prostaglandin D3)

SMILES for HMDB0003034 (Prostaglandin D3)

INCHI for HMDB0003034 (Prostaglandin D3)

Structure for HMDB0003034 (Prostaglandin D3)

3D Structure for HMDB0003034 (Prostaglandin D3)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra