Showing metabocard for Prostaglandin D1 (BMDB0005102)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:15:28 UTC
Update Date2020-04-22 15:15:23 UTC
BMDB IDBMDB0005102
Secondary Accession Numbers
  • BMDB05102
Metabolite Identification
Common NameProstaglandin D1
DescriptionProstaglandin D1, also known as PGD1, 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 D1 is considered to be an eicosanoid. Based on a literature review a small amount of articles have been published on Prostaglandin D1.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
5-Hydroxy-2-(3-hydroxy-1-octenyl)-3-oxocyclopentaneheptanoic acidChEBI
PGD1ChEBI
5-Hydroxy-2-(3-hydroxy-1-octenyl)-3-oxocyclopentaneheptanoateGenerator
(13E,15S)-9alpha,15-Dihydroxy-11-oxoprost-13-en-1-OateHMDB
(13E,15S)-9alpha,15-Dihydroxy-11-oxoprost-13-en-1-Oic acidHMDB
11-dehydro-Prostaglandin F1aHMDB
2-Hydroxy-5-(3S-hydroxy-1-octenyl)-3-oxocyclopentaneheptanoateHMDB
2-Hydroxy-5-(3S-hydroxy-1-octenyl)-3-oxocyclopentaneheptanoic acidHMDB
5-Hydroxy-2-(3-hydroxy-1-octenyl)-3-oxo-cyclopentaneheptanoateHMDB
5-Hydroxy-2-(3-hydroxy-1-octenyl)-3-oxo-cyclopentaneheptanoic acidHMDB
9a,15-Dihydroxy-11-ketoprost-13-enoateHMDB
9a,15-Dihydroxy-11-ketoprost-13-enoic acidHMDB
9S,15S-Dihydroxy-11-oxo-13E-prostaenoateHMDB
9S,15S-Dihydroxy-11-oxo-13E-prostaenoic acidHMDB
Prostaglandin D1MeSH
Chemical FormulaC20H34O5
Average Molecular Weight354.481
Monoisotopic Molecular Weight354.240624198
IUPAC Name7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]heptanoic acid
Traditional Nameprostaglandin D1
CAS Registry Number17968-82-0
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 KeyCIMMACURCPXICP-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.
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
  • 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 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
LogP3.172Not Available
Predicted Properties
PropertyValueSource
logP3.12ALOGPS
logP3.59ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)4.45ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count13ChemAxon
Refractivity98.32 m³·mol⁻¹ChemAxon
Polarizability42.16 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, Positivesplash10-01p6-7394000000-61a4beceef991ea7edf5View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0a4l-7452690000-131fa87991aed048b420View 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, Positivesplash10-00kr-0019000000-9d8624d18460cdecefcdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01bl-4498000000-f0750b2254496b1f4fe3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-06du-9220000000-b45f534ddf2305427910View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udr-0009000000-3140cbab7c81db32101bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0f79-1039000000-5cd765494d3c1f121b28View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9631000000-9734107df1c16fb89916View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0009000000-1746d3de0ce6f836b391View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014i-7096000000-82c8788991fe0c03e762View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-05mo-9300000000-2fd7048bfc7fd607df6dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0fri-0009000000-f7da3faa61631ece5363View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fri-0049000000-dbee20d47da23ed3d477View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-002g-9153000000-3d01e42c9dfef3eb1e86View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0005102
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023631
KNApSAcK IDNot Available
Chemspider ID4444438
KEGG Compound IDC06438
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5280936
PDB IDNot Available
ChEBI ID27696
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available