Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-10-25 15:06:25 UTC

Update Date

2022-09-22 17:43:53 UTC

HMDB ID

HMDB0005102

Secondary Accession Numbers

HMDB05102

Metabolite Identification

Common Name

Prostaglandin D1

Description

Prostaglandin D1 is a prostanoid that elicits contractile and relaxant on isolated human pial arteries with small potency. Prostanoids is a term that collectively describes prostaglandins, prostacyclines and thromboxanes. 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: 6091419 , 16986207 )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

HMDB0005102
     RDKit          3D
Prostaglandin D1
 59 59  0  0  0  0  0  0  0  0999 V2000
   -4.1291   -2.8620   -2.9195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5425   -2.3289   -1.5848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4038   -0.7951   -1.5712 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8244   -0.2968   -0.2160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7640    1.1724   -0.0214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4237    1.8038   -0.1935 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9362    1.6007   -1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4215    1.2530    0.7720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1428    1.5673    0.6940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1374    1.0044    1.6739 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8168    0.0276    2.5191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3326    0.1972    3.6056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7774   -1.2739    1.8067 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2093   -1.0979    0.6947 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1502   -2.1427    0.8127 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8537    0.2547    0.8971 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1958    0.0552    1.4967 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9525    1.3023    1.8174 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1984    2.1608    0.5977 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9927    1.4564   -0.4745 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3522    1.0295    0.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1374    0.3355   -1.0627 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4796   -0.8871   -1.5709 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5077   -0.8267   -2.3906 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9193   -2.1339   -1.1545 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0756   -3.2542   -2.9116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0921   -2.0248   -3.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8005   -3.6335   -3.3357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8986   -2.7709   -0.7901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5859   -2.6390   -1.3961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0688   -0.4099   -2.3526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3286   -0.6185   -1.7952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2146   -0.8459    0.5403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8775   -0.6763   -0.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5228    1.7066   -0.6443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0838    1.3643    1.0469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4542    2.8990   -0.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6940    1.7964   -2.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7459    0.5729    1.5672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7999    2.2480   -0.0932 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2348    1.8948    2.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4600   -2.0358    2.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7420   -1.5885    1.3874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2397   -1.2259   -0.3095 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8603   -2.9372    0.2987 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9345    0.7014   -0.1309 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1326   -0.5667    2.4120 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8071   -0.5261    0.7730 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9455    1.0299    2.2266 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4687    1.9499    2.5670 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2418    2.5045    0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8118    3.0294    0.9395 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1191    2.1503   -1.3212 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4607    0.5443   -0.8380 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9376    1.9018    0.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2622    0.3027    0.8568 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2866    1.0097   -1.9442 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1568    0.0774   -0.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7277   -2.5062   -0.2137 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  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  1  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
  3 32  1  0
  4 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  6 37  1  1
  7 38  1  0
  8 39  1  0
  9 40  1  0
 10 41  1  1
 13 42  1  0
 13 43  1  0
 14 44  1  6
 15 45  1  0
 16 46  1  6
 17 47  1  0
 17 48  1  0
 18 49  1  0
 18 50  1  0
 19 51  1  0
 19 52  1  0
 20 53  1  0
 20 54  1  0
 21 55  1  0
 21 56  1  0
 22 57  1  0
 22 58  1  0
 25 59  1  0
M  END

  Mrv0541 02231220212D          

 25 25  0  0  1  0            999 V2000
   18.3463  -10.2499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.6958   -8.5429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2438   -5.8379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9853   -9.9862    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4268   -8.6272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5763   -8.7979    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.2438   -8.3129    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.8313   -9.5825    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.7917   -8.5429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.6563   -9.5825    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9112   -8.7979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1785   -9.0950    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2438   -7.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3939   -8.8400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9582   -7.0754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7808   -9.3920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9582   -6.2504    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.9961   -9.1371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.6726   -5.8379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.6726   -5.0128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3830   -9.6891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3872   -4.6003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3872   -3.7753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5984   -9.4342    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1016   -3.3628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  2 11  2  0  0  0  0
 17  3  1  1  0  0  0
  4 24  1  0  0  0  0
  5 24  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  1  6  0  0  0
  7 11  1  0  0  0  0
  7 13  1  1  0  0  0
  8 10  1  0  0  0  0
  9 12  1  0  0  0  0
 10 11  1  0  0  0  0
 12 14  1  0  0  0  0
 13 15  2  0  0  0  0
 14 16  1  0  0  0  0
 15 17  1  0  0  0  0
 16 18  1  0  0  0  0
 17 19  1  0  0  0  0
 18 21  1  0  0  0  0
 19 20  1  0  0  0  0
 20 22  1  0  0  0  0
 21 24  1  0  0  0  0
 22 23  1  0  0  0  0
 23 25  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0005102

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](CCCCCCC(O)=O)[C@@H](O)CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H34O5/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/h12-13,15-18,21-22H,2-11,14H2,1H3,(H,24,25)/b13-12+/t15-,16+,17+,18-/m0/s1

> <INCHI_KEY>
CIMMACURCPXICP-PNQRDDRVSA-N

> <FORMULA>
C20H34O5

> <MOLECULAR_WEIGHT>
354.481

> <EXACT_MASS>
354.240624198

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
42.16119306962469

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]heptanoic acid

> <ALOGPS_LOGP>
3.12

> <JCHEM_LOGP>
3.5871917936666664

> <ALOGPS_LOGS>
-3.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.193507592941653

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.454206478024355

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5973978434836424

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
98.31849999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.55e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
prostaglandin D1

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0005102
     RDKit          3D
Prostaglandin D1
 59 59  0  0  0  0  0  0  0  0999 V2000
   -4.1291   -2.8620   -2.9195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5425   -2.3289   -1.5848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4038   -0.7951   -1.5712 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8244   -0.2968   -0.2160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7640    1.1724   -0.0214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4237    1.8038   -0.1935 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9362    1.6007   -1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4215    1.2530    0.7720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1428    1.5673    0.6940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1374    1.0044    1.6739 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8168    0.0276    2.5191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3326    0.1972    3.6056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7774   -1.2739    1.8067 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2093   -1.0979    0.6947 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1502   -2.1427    0.8127 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8537    0.2547    0.8971 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1958    0.0552    1.4967 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9525    1.3023    1.8174 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1984    2.1608    0.5977 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9927    1.4564   -0.4745 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3522    1.0295    0.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1374    0.3355   -1.0627 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4796   -0.8871   -1.5709 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5077   -0.8267   -2.3906 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9193   -2.1339   -1.1545 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0756   -3.2542   -2.9116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0921   -2.0248   -3.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8005   -3.6335   -3.3357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8986   -2.7709   -0.7901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5859   -2.6390   -1.3961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0688   -0.4099   -2.3526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3286   -0.6185   -1.7952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2146   -0.8459    0.5403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8775   -0.6763   -0.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5228    1.7066   -0.6443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0838    1.3643    1.0469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4542    2.8990   -0.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6940    1.7964   -2.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7459    0.5729    1.5672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7999    2.2480   -0.0932 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2348    1.8948    2.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4600   -2.0358    2.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7420   -1.5885    1.3874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2397   -1.2259   -0.3095 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8603   -2.9372    0.2987 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9345    0.7014   -0.1309 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1326   -0.5667    2.4120 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8071   -0.5261    0.7730 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9455    1.0299    2.2266 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4687    1.9499    2.5670 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2418    2.5045    0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8118    3.0294    0.9395 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1191    2.1503   -1.3212 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4607    0.5443   -0.8380 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9376    1.9018    0.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2622    0.3027    0.8568 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2866    1.0097   -1.9442 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1568    0.0774   -0.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7277   -2.5062   -0.2137 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  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  1  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
  3 32  1  0
  4 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  6 37  1  1
  7 38  1  0
  8 39  1  0
  9 40  1  0
 10 41  1  1
 13 42  1  0
 13 43  1  0
 14 44  1  6
 15 45  1  0
 16 46  1  6
 17 47  1  0
 17 48  1  0
 18 49  1  0
 18 50  1  0
 19 51  1  0
 19 52  1  0
 20 53  1  0
 20 54  1  0
 21 55  1  0
 21 56  1  0
 22 57  1  0
 22 58  1  0
 25 59  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      34.246 -19.133   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      38.632 -15.947   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      35.922 -10.897   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      24.239 -18.641   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      25.063 -16.104   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      34.676 -16.423   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      35.922 -15.517   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      35.152 -17.887   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      33.211 -15.947   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      36.692 -17.887   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      37.168 -16.423   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      32.067 -16.977   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      35.922 -13.977   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      30.602 -16.501   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      37.255 -13.207   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      29.457 -17.532   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      37.255 -11.667   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      27.993 -17.056   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      38.589 -10.897   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      38.589  -9.357   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      26.848 -18.086   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      39.923  -8.587   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      39.923  -7.047   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      25.384 -17.611   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      41.256  -6.277   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2   11                                                            
CONECT    3   17                                                            
CONECT    4   24                                                            
CONECT    5   24                                                            
CONECT    6    7    8    9                                                  
CONECT    7    6   11   13                                                  
CONECT    8    1    6   10                                                  
CONECT    9    6   12                                                       
CONECT   10    8   11                                                       
CONECT   11    2    7   10                                                  
CONECT   12    9   14                                                       
CONECT   13    7   15                                                       
CONECT   14   12   16                                                       
CONECT   15   13   17                                                       
CONECT   16   14   18                                                       
CONECT   17    3   15   19                                                  
CONECT   18   16   21                                                       
CONECT   19   17   20                                                       
CONECT   20   19   22                                                       
CONECT   21   18   24                                                       
CONECT   22   20   23                                                       
CONECT   23   22   25                                                       
CONECT   24    4    5   21                                                  
CONECT   25   23                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   50    0
END

COMPND    HMDB0005102
HETATM    1  C1  UNL     1      -4.129  -2.862  -2.919  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.542  -2.329  -1.585  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.404  -0.795  -1.571  1.00  0.00           C  
HETATM    4  C4  UNL     1      -4.824  -0.297  -0.216  1.00  0.00           C  
HETATM    5  C5  UNL     1      -4.764   1.172  -0.021  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.424   1.804  -0.193  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.936   1.601  -1.492  1.00  0.00           O  
HETATM    8  C7  UNL     1      -2.422   1.253   0.772  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.143   1.567   0.694  1.00  0.00           C  
HETATM   10  C9  UNL     1      -0.137   1.004   1.674  1.00  0.00           C  
HETATM   11  C10 UNL     1      -0.817   0.028   2.519  1.00  0.00           C  
HETATM   12  O2  UNL     1      -1.333   0.197   3.606  1.00  0.00           O  
HETATM   13  C11 UNL     1      -0.777  -1.274   1.807  1.00  0.00           C  
HETATM   14  C12 UNL     1       0.209  -1.098   0.695  1.00  0.00           C  
HETATM   15  O3  UNL     1       1.150  -2.143   0.813  1.00  0.00           O  
HETATM   16  C13 UNL     1       0.854   0.255   0.897  1.00  0.00           C  
HETATM   17  C14 UNL     1       2.196   0.055   1.497  1.00  0.00           C  
HETATM   18  C15 UNL     1       2.953   1.302   1.817  1.00  0.00           C  
HETATM   19  C16 UNL     1       3.198   2.161   0.598  1.00  0.00           C  
HETATM   20  C17 UNL     1       3.993   1.456  -0.475  1.00  0.00           C  
HETATM   21  C18 UNL     1       5.352   1.029   0.015  1.00  0.00           C  
HETATM   22  C19 UNL     1       6.137   0.336  -1.063  1.00  0.00           C  
HETATM   23  C20 UNL     1       5.480  -0.887  -1.571  1.00  0.00           C  
HETATM   24  O4  UNL     1       4.508  -0.827  -2.391  1.00  0.00           O  
HETATM   25  O5  UNL     1       5.919  -2.134  -1.155  1.00  0.00           O  
HETATM   26  H1  UNL     1      -3.076  -3.254  -2.912  1.00  0.00           H  
HETATM   27  H2  UNL     1      -4.092  -2.025  -3.674  1.00  0.00           H  
HETATM   28  H3  UNL     1      -4.801  -3.633  -3.336  1.00  0.00           H  
HETATM   29  H4  UNL     1      -3.899  -2.771  -0.790  1.00  0.00           H  
HETATM   30  H5  UNL     1      -5.586  -2.639  -1.396  1.00  0.00           H  
HETATM   31  H6  UNL     1      -5.069  -0.410  -2.353  1.00  0.00           H  
HETATM   32  H7  UNL     1      -3.329  -0.619  -1.795  1.00  0.00           H  
HETATM   33  H8  UNL     1      -4.215  -0.846   0.540  1.00  0.00           H  
HETATM   34  H9  UNL     1      -5.878  -0.676  -0.070  1.00  0.00           H  
HETATM   35  H10 UNL     1      -5.523   1.707  -0.644  1.00  0.00           H  
HETATM   36  H11 UNL     1      -5.084   1.364   1.047  1.00  0.00           H  
HETATM   37  H12 UNL     1      -3.454   2.899  -0.033  1.00  0.00           H  
HETATM   38  H13 UNL     1      -3.694   1.796  -2.116  1.00  0.00           H  
HETATM   39  H14 UNL     1      -2.746   0.573   1.567  1.00  0.00           H  
HETATM   40  H15 UNL     1      -0.800   2.248  -0.093  1.00  0.00           H  
HETATM   41  H16 UNL     1       0.235   1.895   2.212  1.00  0.00           H  
HETATM   42  H17 UNL     1      -0.460  -2.036   2.551  1.00  0.00           H  
HETATM   43  H18 UNL     1      -1.742  -1.588   1.387  1.00  0.00           H  
HETATM   44  H19 UNL     1      -0.240  -1.226  -0.310  1.00  0.00           H  
HETATM   45  H20 UNL     1       0.860  -2.937   0.299  1.00  0.00           H  
HETATM   46  H21 UNL     1       0.935   0.701  -0.131  1.00  0.00           H  
HETATM   47  H22 UNL     1       2.133  -0.567   2.412  1.00  0.00           H  
HETATM   48  H23 UNL     1       2.807  -0.526   0.773  1.00  0.00           H  
HETATM   49  H24 UNL     1       3.945   1.030   2.227  1.00  0.00           H  
HETATM   50  H25 UNL     1       2.469   1.950   2.567  1.00  0.00           H  
HETATM   51  H26 UNL     1       2.242   2.505   0.145  1.00  0.00           H  
HETATM   52  H27 UNL     1       3.812   3.029   0.939  1.00  0.00           H  
HETATM   53  H28 UNL     1       4.119   2.150  -1.321  1.00  0.00           H  
HETATM   54  H29 UNL     1       3.461   0.544  -0.838  1.00  0.00           H  
HETATM   55  H30 UNL     1       5.938   1.902   0.373  1.00  0.00           H  
HETATM   56  H31 UNL     1       5.262   0.303   0.857  1.00  0.00           H  
HETATM   57  H32 UNL     1       6.287   1.010  -1.944  1.00  0.00           H  
HETATM   58  H33 UNL     1       7.157   0.077  -0.692  1.00  0.00           H  
HETATM   59  H34 UNL     1       5.728  -2.506  -0.214  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3   29   30
CONECT    3    4   31   32
CONECT    4    5   33   34
CONECT    5    6   35   36
CONECT    6    7    8   37
CONECT    7   38
CONECT    8    9    9   39
CONECT    9   10   40
CONECT   10   11   16   41
CONECT   11   12   12   13
CONECT   13   14   42   43
CONECT   14   15   16   44
CONECT   15   45
CONECT   16   17   46
CONECT   17   18   47   48
CONECT   18   19   49   50
CONECT   19   20   51   52
CONECT   20   21   53   54
CONECT   21   22   55   56
CONECT   22   23   57   58
CONECT   23   24   24   25
CONECT   25   59
END

HMDB0005102
     RDKit          3D
Prostaglandin D1
 59 59  0  0  0  0  0  0  0  0999 V2000
   -4.1291   -2.8620   -2.9195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5425   -2.3289   -1.5848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4038   -0.7951   -1.5712 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8244   -0.2968   -0.2160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7640    1.1724   -0.0214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4237    1.8038   -0.1935 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9362    1.6007   -1.4922 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4215    1.2530    0.7720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1428    1.5673    0.6940 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1374    1.0044    1.6739 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8168    0.0276    2.5191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3326    0.1972    3.6056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7774   -1.2739    1.8067 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2093   -1.0979    0.6947 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1502   -2.1427    0.8127 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8537    0.2547    0.8971 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1958    0.0552    1.4967 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9525    1.3023    1.8174 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1984    2.1608    0.5977 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9927    1.4564   -0.4745 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3522    1.0295    0.0148 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1374    0.3355   -1.0627 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4796   -0.8871   -1.5709 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5077   -0.8267   -2.3906 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9193   -2.1339   -1.1545 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0756   -3.2542   -2.9116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0921   -2.0248   -3.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8005   -3.6335   -3.3357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8986   -2.7709   -0.7901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5859   -2.6390   -1.3961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0688   -0.4099   -2.3526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3286   -0.6185   -1.7952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2146   -0.8459    0.5403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8775   -0.6763   -0.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5228    1.7066   -0.6443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0838    1.3643    1.0469 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4542    2.8990   -0.0328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6940    1.7964   -2.1155 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7459    0.5729    1.5672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7999    2.2480   -0.0932 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2348    1.8948    2.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4600   -2.0358    2.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7420   -1.5885    1.3874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2397   -1.2259   -0.3095 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8603   -2.9372    0.2987 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9345    0.7014   -0.1309 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1326   -0.5667    2.4120 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8071   -0.5261    0.7730 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9455    1.0299    2.2266 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4687    1.9499    2.5670 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2418    2.5045    0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8118    3.0294    0.9395 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1191    2.1503   -1.3212 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4607    0.5443   -0.8380 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9376    1.9018    0.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2622    0.3027    0.8568 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2866    1.0097   -1.9442 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1568    0.0774   -0.6918 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7277   -2.5062   -0.2137 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  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  1  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
  3 32  1  0
  4 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  6 37  1  1
  7 38  1  0
  8 39  1  0
  9 40  1  0
 10 41  1  1
 13 42  1  0
 13 43  1  0
 14 44  1  6
 15 45  1  0
 16 46  1  6
 17 47  1  0
 17 48  1  0
 18 49  1  0
 18 50  1  0
 19 51  1  0
 19 52  1  0
 20 53  1  0
 20 54  1  0
 21 55  1  0
 21 56  1  0
 22 57  1  0
 22 58  1  0
 25 59  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5-Hydroxy-2-(3-hydroxy-1-octenyl)-3-oxocyclopentaneheptanoic acid	ChEBI
PGD1	ChEBI
5-Hydroxy-2-(3-hydroxy-1-octenyl)-3-oxocyclopentaneheptanoate	Generator
(13E,15S)-9alpha,15-Dihydroxy-11-oxoprost-13-en-1-Oate	HMDB
(13E,15S)-9alpha,15-Dihydroxy-11-oxoprost-13-en-1-Oic acid	HMDB
11-dehydro-Prostaglandin F1a	HMDB
2-Hydroxy-5-(3S-hydroxy-1-octenyl)-3-oxocyclopentaneheptanoate	HMDB
2-Hydroxy-5-(3S-hydroxy-1-octenyl)-3-oxocyclopentaneheptanoic acid	HMDB
5-Hydroxy-2-(3-hydroxy-1-octenyl)-3-oxo-cyclopentaneheptanoate	HMDB
5-Hydroxy-2-(3-hydroxy-1-octenyl)-3-oxo-cyclopentaneheptanoic acid	HMDB
9a,15-Dihydroxy-11-ketoprost-13-enoate	HMDB
9a,15-Dihydroxy-11-ketoprost-13-enoic acid	HMDB
9S,15S-Dihydroxy-11-oxo-13E-prostaenoate	HMDB
9S,15S-Dihydroxy-11-oxo-13E-prostaenoic acid	HMDB
Prostaglandin D1	MeSH

Chemical Formula

C₂₀H₃₄O₅

Average Molecular Weight

354.481

Monoisotopic Molecular Weight

354.240624198

IUPAC Name

7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]heptanoic acid

Traditional Name

prostaglandin D1

CAS Registry Number

17968-82-0

SMILES

CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](CCCCCCC(O)=O)[C@@H](O)CC1=O

InChI Identifier

InChI=1S/C20H34O5/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/h12-13,15-18,21-22H,2-11,14H2,1H3,(H,24,25)/b13-12+/t15-,16+,17+,18-/m0/s1

InChI Key

CIMMACURCPXICP-PNQRDDRVSA-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
Fatty alcohol
Hydroxy fatty acid
Cyclopentanol
Cyclic alcohol
Cyclic ketone
Ketone
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Organooxygen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

prostaglandins D (CHEBI:27696 )
Prostaglandins (C06438 )
Prostaglandins (LMFA03010049 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 20671299)

Cellular substructure

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0005102)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0005102)

Source

Endogenous

Endogenous (HMDB: HMDB0005102)

Animal

Animal (HMDB: HMDB0005102)

Exogenous

Food

Food (HMDB: HMDB0005102)

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)

Exogenous (HMDB: HMDB0005102)

Process

Role

Biological role

Membrane stabilizer (HMDB: HMDB0005102)

Modulator

Immunomodulator (HMDB: HMDB0005102)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0005102)

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	3.172	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.076 g/L	ALOGPS
logP	3.12	ALOGPS
logP	3.59	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	4.45	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	13	ChemAxon
Refractivity	98.32 m³·mol⁻¹	ChemAxon
Polarizability	42.16 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]+	188.23	31661259
DarkChem	[M-H]-	189.413	31661259
DeepCCS	[M+H]+	203.724	30932474
DeepCCS	[M-H]-	201.366	30932474
DeepCCS	[M-2H]-	235.233	30932474
DeepCCS	[M+Na]+	210.461	30932474
AllCCS	[M+H]+	194.1	32859911
AllCCS	[M+H-H2O]+	191.5	32859911
AllCCS	[M+NH4]+	196.6	32859911
AllCCS	[M+Na]+	197.2	32859911
AllCCS	[M-H]-	192.3	32859911
AllCCS	[M+Na-2H]-	193.6	32859911
AllCCS	[M+HCOO]-	195.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Prostaglandin D1	CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](CCCCCCC(O)=O)[C@@H](O)CC1=O	4341.3	Standard polar	33892256
Prostaglandin D1	CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](CCCCCCC(O)=O)[C@@H](O)CC1=O	2718.7	Standard non polar	33892256
Prostaglandin D1	CCCCC[C@H](O)\C=C\[C@@H]1[C@@H](CCCCCCC(O)=O)[C@@H](O)CC1=O	2841.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Prostaglandin D1,1TMS,isomer #1	CCCCC[C@@H](/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C	2816.4	Semi standard non polar	33892256
Prostaglandin D1,1TMS,isomer #2	CCCCC[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C	2783.6	Semi standard non polar	33892256
Prostaglandin D1,1TMS,isomer #3	CCCCC[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O	2750.9	Semi standard non polar	33892256
Prostaglandin D1,1TMS,isomer #4	CCCCC[C@H](O)/C=C/C1=C(O[Si](C)(C)C)C[C@H](O)[C@@H]1CCCCCCC(=O)O	2909.0	Semi standard non polar	33892256
Prostaglandin D1,1TMS,isomer #5	CCCCC[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1CCCCCCC(=O)O	2740.7	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #1	CCCCC[C@@H](/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C	2757.1	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #2	CCCCC[C@@H](/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2809.2	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #3	CCCCC[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C	2971.9	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #4	CCCCC[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C	2791.9	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #5	CCCCC[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C	2734.6	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #6	CCCCC[C@H](O)/C=C/C1=C(O[Si](C)(C)C)C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C	2916.6	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #7	CCCCC[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C	2757.4	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #8	CCCCC[C@H](O)/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O	2905.2	Semi standard non polar	33892256
Prostaglandin D1,2TMS,isomer #9	CCCCC[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O	2789.9	Semi standard non polar	33892256
Prostaglandin D1,3TMS,isomer #1	CCCCC[C@@H](/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2743.5	Semi standard non polar	33892256
Prostaglandin D1,3TMS,isomer #2	CCCCC[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C	2928.8	Semi standard non polar	33892256
Prostaglandin D1,3TMS,isomer #3	CCCCC[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C	2827.2	Semi standard non polar	33892256
Prostaglandin D1,3TMS,isomer #4	CCCCC[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2952.5	Semi standard non polar	33892256
Prostaglandin D1,3TMS,isomer #5	CCCCC[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2806.6	Semi standard non polar	33892256
Prostaglandin D1,3TMS,isomer #6	CCCCC[C@H](O)/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C	2900.1	Semi standard non polar	33892256
Prostaglandin D1,3TMS,isomer #7	CCCCC[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C	2796.4	Semi standard non polar	33892256
Prostaglandin D1,4TMS,isomer #1	CCCCC[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2905.2	Semi standard non polar	33892256
Prostaglandin D1,4TMS,isomer #1	CCCCC[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2818.4	Standard non polar	33892256
Prostaglandin D1,4TMS,isomer #1	CCCCC[C@@H](/C=C/C1=C(O[Si](C)(C)C)C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2981.0	Standard polar	33892256
Prostaglandin D1,4TMS,isomer #2	CCCCC[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2859.7	Semi standard non polar	33892256
Prostaglandin D1,4TMS,isomer #2	CCCCC[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	2725.6	Standard non polar	33892256
Prostaglandin D1,4TMS,isomer #2	CCCCC[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C	3017.8	Standard polar	33892256
Prostaglandin D1,1TBDMS,isomer #1	CCCCC[C@@H](/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C	3062.7	Semi standard non polar	33892256
Prostaglandin D1,1TBDMS,isomer #2	CCCCC[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C	3037.4	Semi standard non polar	33892256
Prostaglandin D1,1TBDMS,isomer #3	CCCCC[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1CCCCCCC(=O)O	2969.3	Semi standard non polar	33892256
Prostaglandin D1,1TBDMS,isomer #4	CCCCC[C@H](O)/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O)[C@@H]1CCCCCCC(=O)O	3123.0	Semi standard non polar	33892256
Prostaglandin D1,1TBDMS,isomer #5	CCCCC[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1CCCCCCC(=O)O	2980.8	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #1	CCCCC[C@@H](/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C	3220.6	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #2	CCCCC[C@@H](/C=C/[C@H]1C(=O)C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3318.1	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #3	CCCCC[C@@H](/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C	3405.5	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #4	CCCCC[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1CCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C	3276.6	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #5	CCCCC[C@H](O)/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C	3204.0	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #6	CCCCC[C@H](O)/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C	3345.1	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #7	CCCCC[C@H](O)/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C	3245.4	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #8	CCCCC[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]1CCCCCCC(=O)O	3316.4	Semi standard non polar	33892256
Prostaglandin D1,2TBDMS,isomer #9	CCCCC[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]1CCCCCCC(=O)O	3239.8	Semi standard non polar	33892256
Prostaglandin D1,3TBDMS,isomer #1	CCCCC[C@@H](/C=C/[C@H]1C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3479.8	Semi standard non polar	33892256
Prostaglandin D1,3TBDMS,isomer #2	CCCCC[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]1CCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C	3567.6	Semi standard non polar	33892256
Prostaglandin D1,3TBDMS,isomer #3	CCCCC[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]1CCCCCCC(=O)O)O[Si](C)(C)C(C)(C)C	3523.2	Semi standard non polar	33892256
Prostaglandin D1,3TBDMS,isomer #4	CCCCC[C@@H](/C=C/C1=C(O[Si](C)(C)C(C)(C)C)C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3642.7	Semi standard non polar	33892256
Prostaglandin D1,3TBDMS,isomer #5	CCCCC[C@@H](/C=C/[C@H]1C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3542.9	Semi standard non polar	33892256
Prostaglandin D1,3TBDMS,isomer #6	CCCCC[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]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C	3535.6	Semi standard non polar	33892256
Prostaglandin D1,3TBDMS,isomer #7	CCCCC[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]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C	3495.4	Semi standard non polar	33892256
Prostaglandin D1,4TBDMS,isomer #1	CCCCC[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]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3767.6	Semi standard non polar	33892256
Prostaglandin D1,4TBDMS,isomer #1	CCCCC[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]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3432.7	Standard non polar	33892256
Prostaglandin D1,4TBDMS,isomer #1	CCCCC[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]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3289.2	Standard polar	33892256
Prostaglandin D1,4TBDMS,isomer #2	CCCCC[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]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3739.4	Semi standard non polar	33892256
Prostaglandin D1,4TBDMS,isomer #2	CCCCC[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]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3215.3	Standard non polar	33892256
Prostaglandin D1,4TBDMS,isomer #2	CCCCC[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]1CCCCCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	3297.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Prostaglandin D1 GC-MS (Non-derivatized) - 70eV, Positive	splash10-01p6-7394000000-61a4beceef991ea7edf5	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Prostaglandin D1 GC-MS (3 TMS) - 70eV, Positive	splash10-0a4l-7452690000-131fa87991aed048b420	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Prostaglandin D1 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 D1 10V, Positive-QTOF	splash10-00kr-0019000000-9d8624d18460cdecefcd	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 20V, Positive-QTOF	splash10-01bl-4498000000-f0750b2254496b1f4fe3	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 40V, Positive-QTOF	splash10-06du-9220000000-b45f534ddf2305427910	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 10V, Negative-QTOF	splash10-0udr-0009000000-3140cbab7c81db32101b	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 20V, Negative-QTOF	splash10-0f79-1039000000-5cd765494d3c1f121b28	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 40V, Negative-QTOF	splash10-0a4i-9631000000-9734107df1c16fb89916	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 10V, Positive-QTOF	splash10-014i-0009000000-1746d3de0ce6f836b391	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 20V, Positive-QTOF	splash10-014i-7096000000-82c8788991fe0c03e762	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 40V, Positive-QTOF	splash10-05mo-9300000000-2fd7048bfc7fd607df6d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 10V, Negative-QTOF	splash10-0fri-0009000000-f7da3faa61631ece5363	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 20V, Negative-QTOF	splash10-0fri-0049000000-dbee20d47da23ed3d477	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Prostaglandin D1 40V, Negative-QTOF	splash10-002g-9153000000-3d01e42c9dfef3eb1e86	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood
Urine

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	0.00001 +/- 0.000001 uM	Adult (>18 years old)	Both	Normal	20671299	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Cancer patients undergoing total body irradiation	31424920	details

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

FDB023631

KNApSAcK ID

Not Available

Chemspider ID

4444438

KEGG Compound ID

C06438

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5280936

PDB ID

Not Available

ChEBI ID

27696

Food Biomarker Ontology

Not Available

VMH ID

HC02208

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Uski TK, Andersson KE, Brandt L, Ljunggren B: Characterization of the prostanoid receptors and of the contractile effects of prostaglandin F2 alpha in human pial arteries. Acta Physiol Scand. 1984 Aug;121(4):369-78. [PubMed:6091419 ]
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 ]
Lipid Maps (LMFA03010049) [Link]

Showing metabocard for Prostaglandin D1 (HMDB0005102)

MOL for HMDB0005102 (Prostaglandin D1)

3D MOL for HMDB0005102 (Prostaglandin D1)

3D SDF for HMDB0005102 (Prostaglandin D1)

3D-SDF for HMDB0005102 (Prostaglandin D1)

PDB for HMDB0005102 (Prostaglandin D1)

3D PDB for HMDB0005102 (Prostaglandin D1)

SMILES for HMDB0005102 (Prostaglandin D1)

INCHI for HMDB0005102 (Prostaglandin D1)

Structure for HMDB0005102 (Prostaglandin D1)

3D Structure for HMDB0005102 (Prostaglandin D1)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra