Showing metabocard for Prostaglandin D3 (BMDB0003034)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:02:31 UTC
Update Date2020-04-22 15:11:38 UTC
BMDB IDBMDB0003034
Secondary Accession Numbers
  • BMDB03034
Metabolite Identification
Common NameProstaglandin D3
DescriptionProstaglandin D3, also known as PGD3, 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. Thus, prostaglandin D3 is considered to be an eicosanoid. Based on a literature review a significant number of articles have been published on Prostaglandin D3.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(5Z)-7-[(1R,2R,5S)-5-Hydroxy-2-[(1E,3S,5Z)-3-hydroxyocta-1,5-dien-1-yl]-3-oxocyclopentyl]hept-5-enoic acidChEBI
(5Z,13E,15S,17Z)-9alpha,15-Dihydroxy-11-oxoprosta-5,13,17-trien-1-Oic acidChEBI
9S,15S-Dihydroxy-11-oxo-5Z,13E,17Z-prostatrienoic acidChEBI
(5Z)-7-[(1R,2R,5S)-5-Hydroxy-2-[(1E,3S,5Z)-3-hydroxyocta-1,5-dien-1-yl]-3-oxocyclopentyl]hept-5-enoateGenerator
(5Z,13E,15S,17Z)-9a,15-Dihydroxy-11-oxoprosta-5,13,17-trien-1-OateGenerator
(5Z,13E,15S,17Z)-9a,15-Dihydroxy-11-oxoprosta-5,13,17-trien-1-Oic acidGenerator
(5Z,13E,15S,17Z)-9alpha,15-Dihydroxy-11-oxoprosta-5,13,17-trien-1-OateGenerator
(5Z,13E,15S,17Z)-9Α,15-dihydroxy-11-oxoprosta-5,13,17-trien-1-OateGenerator
(5Z,13E,15S,17Z)-9Α,15-dihydroxy-11-oxoprosta-5,13,17-trien-1-Oic acidGenerator
9S,15S-Dihydroxy-11-oxo-5Z,13E,17Z-prostatrienoateGenerator
PGD3HMDB
Prostaglandin D3MeSH
Chemical FormulaC20H30O5
Average Molecular Weight350.4492
Monoisotopic Molecular Weight350.20932407
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 Nameprostaglandin D3
CAS Registry Number71902-47-1
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 KeyANOICLBSJIMQTA-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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassEicosanoids
Direct ParentProstaglandins 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 FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.88ALOGPS
logP2.86ChemAxon
logS-3.6ALOGPS
pKa (Strongest Acidic)4.4ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity100.55 m³·mol⁻¹ChemAxon
Polarizability39.67 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05po-8395000000-44ba79a27b1cb029e065View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0udi-3620690000-cee4d57fecd9b1501065View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00lr-0019000000-556c5941c1bd947aa13dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0159-3096000000-7308f804ecfd913b1984View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014r-9310000000-135a6bbfabaf1b739b8aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000t-0009000000-50f3213aa3eff0d0faf7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001j-2149000000-89d63bd18af619a97e66View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9531000000-1f37f093b3d2f8ec45afView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000t-0009000000-669e3ea846c980353bebView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06rt-0059000000-3be047d22831afb5d0f0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052p-9441000000-6a5fd85e6df4f33930aeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0019000000-928cd476df97ec2d1eb4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-4194000000-7014986c36784cd7e024View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-05mo-9310000000-3fcdcc5aa45a25f6dab0View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0003034
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023097
KNApSAcK IDNot Available
Chemspider ID4445434
KEGG Compound IDC13802
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID2560
PubChem Compound5282260
PDB IDNot Available
ChEBI ID34939
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available