Human Metabolome Database Version 3.5

Showing metabocard for Prostaglandin D2 (HMDB01403)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-05-29 13:31:26 -0600
HMDB ID HMDB01403
Secondary Accession Numbers None
Metabolite Identification
Common Name Prostaglandin D2
Description Prostaglandin D2 (or PGD2) is a prostaglandin that is actively produced in various organs such as the brain, spleen, thymus, bone marrow, uterus, ovary, oviduct, testis, prostate and epididymis, and is involved in many physiological events. PGD2 binds to the prostaglandin D2 receptor (PTGDR) which is a G-protein-coupled receptor. Its activity is mainly mediated by G-S proteins that stimulate adenylate cyclase resulting in an elevation of intracellular cAMP and Ca2+. PGD2 promotes sleep; regulates body temperature, olfactory function, hormone release, and nociception in the central nervous system; prevents platelet aggregation; and induces vasodilation and bronchoconstriction. PGD2 is also released from mast cells as an allergic and inflammatory mediator. Prostaglandin H2 is an unstable intermediate formed from PGG2 by the action of cyclooxygenase (COX) in the arachidonate cascade. In mammalian systems, it is efficiently converted into more stable arachidonate metabolites, such as PGD2, PGE2, PGF2a by the action of three groups of enzymes, PGD synthases (PGDS), PGE synthases and PGF synthases, respectively. PGDS catalyzes the isomerization of PGH2 to PGD2. Two types of PGD2 synthase are known. Lipocalin-type PGD synthase is present in cerebrospinal fluid, seminal plasma and may play an important role in male reproduction. Another PGD synthase, hematopoietic PGD synthase is present in the spleen, fallopian tube, endometrial gland cells, extravillous trophoblasts and villous trophoblasts, and perhaps plays an important role in female reproduction. Recent studies demonstrate that PGD2 is probably involved in multiple aspects of inflammation through its dual receptor systems, DP and CRTH2. (PMID: 12148545 Link_out)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 signaling pathways.
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. (5Z,13E)-(15S)-9,15-dihydroxy-11-oxoprosta-5,13-dienoate
  2. (5Z,13E)-(15S)-9,15-dihydroxy-11-oxoprosta-5,13-dienoic acid
  3. (5z,13e)-(15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
  4. (5z,13e)-(15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoic acid
  5. (5Z,13E)-(15S)-9a,15-Dihydroxy-11-oxoprosta-5,13-dienoate
  6. (5Z,13E)-(15S)-9a,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid
  7. (5Z,13E)-(15S)-9alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
  8. (5Z,13E)-(15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoic acid
  9. (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
  10. (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoic acid
  11. (5Z,13E,15S)-9a,15-dihydroxy-11-oxoprosta-5,13-dien-1-oate
  12. (5Z,13E,15S)-9a,15-dihydroxy-11-oxoprosta-5,13-dien-1-oic acid
  13. (5Z,9-alpha,13E,15S)-9,15-dihydroxy-11-oxo-Prosta-5,13-dien-1-oate
  14. (5Z,9-alpha,13E,15S)-9,15-dihydroxy-11-oxo-Prosta-5,13-dien-1-oic acid
  15. (5Z,9alpha,13E,15S)-9,15-dihydroxy-11-oxo-prosta-5,13-dien-1-oate
  16. (5Z,9alpha,13E,15S)-9,15-dihydroxy-11-oxo-prosta-5,13-dien-1-oic acid
  17. 11-Dehydroprostaglandin F2-alpha
  18. 11-Dehydroprostaglandin F2alpha
  19. 9S,15S-Dihydroxy-11-oxo-5Z,13E-prostadienoate
  20. 9S,15S-Dihydroxy-11-oxo-5Z,13E-prostadienoic acid
  21. PGD2
  22. Prostaglandin d2
Chemical Formula C20H32O5
Average Molecular Weight 352.4651
Monoisotopic Molecular Weight 352.224974134
IUPAC Name (5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoic acid
Traditional IUPAC Name prostaglandin D2
CAS Registry Number 41598-07-6
SMILES CCCCC[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/C20H32O5/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/h4,7,12-13,15-18,21-22H,2-3,5-6,8-11,14H2,1H3,(H,24,25)/b7-4-,13-12+/t15-,16+,17+,18-/m0/s1
InChI Key BHMBVRSPMRCCGG-OUTUXVNYSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Lipids
Class Eicosanoids
Sub Class Prostaglandins and related compounds
Other Descriptors
  • Aliphatic Homomonocyclic Compounds
  • Carbocyclic Fatty Acids
  • Keto Fatty Acids
  • Organic Compounds
  • Unsaturated Fatty Acids
Substituents
  • Allyl Alcohol
  • Carboxylic Acid
  • Cyclic Alcohol
  • Ketone
  • Secondary Alcohol
Direct Parent Prostaglandins and related compounds
Ontology
Status Detected and Quantified
Origin
  • Endogenous
  • Food
Biofunction
  • Cell signaling
  • Component of Prostaglandin and leukotriene metabolism
  • Fuel and energy storage
  • Fuel or energy source
  • Membrane integrity/stability
Application
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Cytoplasm
  • Extracellular
  • Membrane (predicted from logP)
  • Endoplasmic reticulum
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 56 - 57 °C Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 0.086 g/L ALOGPS
LogP 3.12 ALOGPS
LogP 3.23 ChemAxon
LogS -3.61 ALOGPS
pKa (strongest acidic) 4.4 ChemAxon
pKa (strongest basic) -1.6 ChemAxon
Hydrogen Acceptor Count 5 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 94.83 A2 ChemAxon
Rotatable Bond Count 12 ChemAxon
Refractivity 99.44 ChemAxon
Polarizability 40.73 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge -1 ChemAxon
Spectra
1H NMR Spectrum
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 25
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 35
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 45
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 50
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 55
MS/MS Spectrum LC-ESI-QIT (4000Q TRAP, Applied Biosystems) 60
MS/MS Spectrum GC-MS
MS/MS Spectrum GC-MS
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane (predicted from logP)
  • Endoplasmic reticulum
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
Tissue Location
  • Neuron
  • Liver
  • Brain
  • Skin
  • Adipose Tissue
  • Platelet
  • Spleen
  • Mast Cell
  • Smooth Muscle
Pathways
Name SMPDB Link KEGG Link
Arachidonic Acid Metabolism SMP00075 map00590 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified
0.0002 +/- 6.5E-5 uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
0.000306 +/- 0.000355 uM Adult (>18 years old) Both Comment Normal
Blood Detected and Quantified
0.0726 +/- 0.0058 uM Adult (>18 years old) Not Specified Comment Normal
Blood Detected and Quantified
<0.1 uM Adult (>18 years old) Not Specified Comment Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Cerebrospinal Fluid (CSF) Detected and Quantified 0.000165 (0.000159-0.000170) uM Not Specified Not Specified closed head
Cerebrospinal Fluid (CSF) Detected and Quantified 0.000511 uM Not Specified Not Specified gunshot wound
Cerebrospinal Fluid (CSF) Detected and Quantified 0.000142 +/- 0.000133 uM Not Specified Not Specified hydrocephalus
Cerebrospinal Fluid (CSF) Detected and Quantified 0.000384 (0.000108-0.000880) uM Not Specified Not Specified meningitis
Cerebrospinal Fluid (CSF) Detected and Quantified 0.00321 uM Not Specified Not Specified subarachnoid hemorrhage with cerebral vasospasm
Cerebrospinal Fluid (CSF) Detected and Quantified 1844.18 (595.8-3092.5) uM Adult (>18 years old) Not Specified Subarachnoid Aneurysmal Hemorrhage
Cerebrospinal Fluid (CSF) Detected and Quantified 0.00131 +/- 0.000159 uM Not Specified Not Specified subarachnoid hemorrhage without cerebral vasospasm
Associated Disorders and Diseases
Disease References
Subarachnoid hemorrhage
  • Gaetani P, Rodriguez y Baena R, Vigano T, Crivellari MT: [Prostaglandin D2 in subarachnoid hemorrhage. Biological and diagnostic implications] Riv Patol Nerv Ment. 1983 Jul-Aug;104(4):171-7. Pubmed: 6598516 Link_out
      Associated OMIM IDs
      DrugBank ID Not Available
      DrugBank Metabolite ID Not Available
      Phenol Explorer Compound ID Not Available
      Phenol Explorer Metabolite ID Not Available
      FoodDB ID FDB022602
      KNApSAcK ID Not Available
      Chemspider ID 395250 Link_out
      KEGG Compound ID C00696 Link_out
      BioCyc ID 5Z13E-15S-9-ALPHA15-DIHYDROXY-11-O Link_out
      BiGG ID 35725 Link_out
      Wikipedia Link Prostaglandin D2 Link_out
      NuGOwiki Link HMDB01403 Link_out
      Metagene Link HMDB01403 Link_out
      METLIN ID 6221 Link_out
      PubChem Compound 448457 Link_out
      PDB ID PG2 Link_out
      ChEBI ID 15555 Link_out
      References
      Synthesis Reference Ogawa, Yuji; Nunomoto, Makoto; Shibasaki, Masakatsu. A novel synthesis of prostaglandin D2. Journal of Organic Chemistry (1986), 51(9), 1625-7.
      Material Safety Data Sheet (MSDS) Download (PDF)
      General References
      1. O'Sullivan S, Dahlen B, Dahlen SE, Kumlin M: Increased urinary excretion of the prostaglandin D2 metabolite 9 alpha, 11 beta-prostaglandin F2 after aspirin challenge supports mast cell activation in aspirin-induced airway obstruction. J Allergy Clin Immunol. 1996 Aug;98(2):421-32. Pubmed: 8757220 Link_out
      2. Parsons WG 3rd, Roberts LJ 2nd: Transformation of prostaglandin D2 to isomeric prostaglandin F2 compounds by human eosinophils: a potential mast cell-eosinophil interaction. Adv Prostaglandin Thromboxane Leukot Res. 1989;19:499-502. Pubmed: 2526527 Link_out
      3. Parsons WG 3rd, Roberts LJ 2nd: Transformation of prostaglandin D2 to isomeric prostaglandin F2 compounds by human eosinophils. A potential mast cell-eosinophil interaction. J Immunol. 1988 Oct 1;141(7):2413-9. Pubmed: 3139758 Link_out
      4. Cooper B: Diminished platelet adenylate cyclase activation by prostaglandin D2 in acute thrombosis. Blood. 1979 Sep;54(3):684-93. Pubmed: 380688 Link_out
      5. Bushfield M, McNicol A, MacIntyre DE: Inhibition of platelet-activating-factor-induced human platelet activation by prostaglandin D2. Differential sensitivity of platelet transduction processes and functional responses to inhibition by cyclic AMP. Biochem J. 1985 Nov 15;232(1):267-71. Pubmed: 3002327 Link_out
      6. Awad JA, Morrow JD, Roberts LJ 2nd: Detection of the major urinary metabolite of prostaglandin D2 in the circulation: demonstration of elevated levels in patients with disorders of systemic mast cell activation. J Allergy Clin Immunol. 1994 May;93(5):817-24. Pubmed: 8182221 Link_out
      7. Wolfe LS, Rostworowski K, Pellerin L, Sherwin A: Metabolism of prostaglandin D2 by human cerebral cortex into 9 alpha, 11 beta-prostaglandin F2 by an active NADPH-dependent 11-ketoreductase. J Neurochem. 1989 Jul;53(1):64-70. Pubmed: 2723663 Link_out
      8. Cutler LS, Christian CP, Feinstein MB: Cytochemical localization of adenylate cyclase in the dense tubule system of human blood platelets stimulated by forskolin, prostacyclin and prostaglandin D2. Biochim Biophys Acta. 1985 Jun 30;845(3):403-10. Pubmed: 3890960 Link_out
      9. Murray JJ, Tonnel AB, Brash AR, Roberts LJ 2nd, Gosset P, Workman R, Capron A, Oates JA: Release of prostaglandin D2 into human airways during acute antigen challenge. N Engl J Med. 1986 Sep 25;315(13):800-4. Pubmed: 3462506 Link_out
      10. Liston TE, Roberts LJ 2nd: Transformation of prostaglandin D2 to 9 alpha, 11 beta-(15S)-trihydroxyprosta-(5Z,13E)-dien-1-oic acid (9 alpha, 11 beta-prostaglandin F2): a unique biologically active prostaglandin produced enzymatically in vivo in humans. Proc Natl Acad Sci U S A. 1985 Sep;82(18):6030-4. Pubmed: 3862115 Link_out
      11. Haberl C, Hultner L, Flugel A, Falk M, Geuenich S, Wilmanns W, Denzlinger C: Release of prostaglandin D2 by murine mast cells: importance of metabolite formation for antiproliferative activity. Mediators Inflamm. 1998;7(2):79-84. Pubmed: 9836493 Link_out
      12. Bate C, Kempster S, Williams A: Prostaglandin D2 mediates neuronal damage by amyloid-beta or prions which activates microglial cells. Neuropharmacology. 2006 Feb;50(2):229-37. Epub 2005 Nov 11. Pubmed: 16289250 Link_out
      13. Nishizawa EE, Miller WL, Gorman RR, Bundy GL, Svensson J, Hamberg M: Prostaglandin d2 as a potential antithrombotic agent. Prostaglandins. 1975 Jan;9(1):109-21. Pubmed: 806102 Link_out
      14. Fuller RW, Dixon CM, Dollery CT, Barnes PJ: Prostaglandin D2 potentiates airway responsiveness to histamine and methacholine. Am Rev Respir Dis. 1986 Feb;133(2):252-4. Pubmed: 3511806 Link_out
      15. Lewis RA, Soter NA, Diamond PT, Austen KF, Oates JA, Roberts LJ 2nd: Prostaglandin D2 generation after activation of rat and human mast cells with anti-IgE. J Immunol. 1982 Oct;129(4):1627-31. Pubmed: 6809826 Link_out
      16. Gresele P, Deckmyn H, Huybrechts E, Vermylen J: Serum albumin enhances the impairment of platelet aggregation with thromboxane synthase inhibition by increasing the formation of prostaglandin D2. Biochem Pharmacol. 1984 Jul 1;33(13):2083-8. Pubmed: 6430299 Link_out
      17. VanderEnde DS, Morrow JD: Release of markedly increased quantities of prostaglandin D2 from the skin in vivo in humans after the application of cinnamic aldehyde. J Am Acad Dermatol. 2001 Jul;45(1):62-7. Pubmed: 11423836 Link_out
      18. Downard CD, Roberts LJ 2nd, Morrow JD: Topical benzoic acid induces the increased biosynthesis of prostaglandin D2 in human skin in vivo. Clin Pharmacol Ther. 1995 Apr;57(4):441-5. Pubmed: 7712673 Link_out
      19. Morrow JD, Minton TA, Awad JA, Roberts LJ: Release of markedly increased quantities of prostaglandin D2 from the skin in vivo in humans following the application of sorbic acid. Arch Dermatol. 1994 Nov;130(11):1408-12. Pubmed: 7979442 Link_out
      20. Morrow JD, Awad JA, Oates JA, Roberts LJ 2nd: Identification of skin as a major site of prostaglandin D2 release following oral administration of niacin in humans. J Invest Dermatol. 1992 May;98(5):812-5. Pubmed: 1373750 Link_out
      21. Saito S, Tsuda H, Michimata T: Prostaglandin D2 and reproduction. Am J Reprod Immunol. 2002 May;47(5):295-302. Pubmed: 12148545 Link_out

      Enzymes
      Name: Hematopoietic prostaglandin D synthase
      Reactions:
      Prostaglandin H2 unknown Prostaglandin D2 details
      Gene Name: HPGDS
      Uniprot ID: O60760 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Prostaglandin-H2 D-isomerase
      Reactions:
      Prostaglandin H2 unknown Prostaglandin D2 details
      Gene Name: PTGDS
      Uniprot ID: P41222 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Prostaglandin D2 receptor
      Reactions: Not Available
      Gene Name: PTGDR
      Uniprot ID: Q13258 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA