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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-09 20:54:45 UTC
Update Date2022-03-07 03:17:39 UTC
HMDB IDHMDB0060103
Secondary Accession Numbers
  • HMDB60103
Metabolite Identification
Common Name9-Deoxy-delta12-PGD2
Description9-Deoxy-delta12-PGD2, also known as 9-deoxy-δ12-PGD2, 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. 9-Deoxy-delta12-PGD2 is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563866015
Synonyms
ValueSource
9-Deoxy-δ12-PGD2Generator
Chemical FormulaC20H32O4
Average Molecular Weight336.4657
Monoisotopic Molecular Weight336.230059512
IUPAC Name(5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoic acid
Traditional Name(5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoic acid
CAS Registry NumberNot Available
SMILES
CCCCC[C@H](O)C\C=C1/[C@@H](C\C=C/CCCC(O)=O)CCC1=O
InChI Identifier
InChI=1S/C20H32O4/c1-2-3-6-10-17(21)13-14-18-16(12-15-19(18)22)9-7-4-5-8-11-20(23)24/h4,7,14,16-17,21H,2-3,5-6,8-13,15H2,1H3,(H,23,24)/b7-4-,18-14+/t16-,17-/m0/s1
InChI KeyJTEYGOLPGOYFJI-GJGHEGAFSA-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
  • Fatty acid
  • Unsaturated fatty acid
  • Ketone
  • Cyclic ketone
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Hydrocarbon derivative
  • Carbonyl group
  • Organooxygen compound
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.03 g/LALOGPS
logP4.45ALOGPS
logP4.43ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)4.63ChemAxon
pKa (Strongest Basic)-1.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count12ChemAxon
Refractivity97.91 m³·mol⁻¹ChemAxon
Polarizability38.63 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+188.29730932474
DeepCCS[M-H]-185.82530932474
DeepCCS[M-2H]-220.23130932474
DeepCCS[M+Na]+195.45830932474
AllCCS[M+H]+189.332859911
AllCCS[M+H-H2O]+186.632859911
AllCCS[M+NH4]+191.932859911
AllCCS[M+Na]+192.632859911
AllCCS[M-H]-189.332859911
AllCCS[M+Na-2H]-190.732859911
AllCCS[M+HCOO]-192.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
9-Deoxy-delta12-PGD2CCCCC[C@H](O)C\C=C1/[C@@H](C\C=C/CCCC(O)=O)CCC1=O4272.1Standard polar33892256
9-Deoxy-delta12-PGD2CCCCC[C@H](O)C\C=C1/[C@@H](C\C=C/CCCC(O)=O)CCC1=O2589.6Standard non polar33892256
9-Deoxy-delta12-PGD2CCCCC[C@H](O)C\C=C1/[C@@H](C\C=C/CCCC(O)=O)CCC1=O2786.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
9-Deoxy-delta12-PGD2,1TMS,isomer #1CCCCC[C@@H](C/C=C1/C(=O)CC[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C2795.5Semi standard non polar33892256
9-Deoxy-delta12-PGD2,1TMS,isomer #2CCCCC[C@H](O)C/C=C1/C(=O)CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C2757.8Semi standard non polar33892256
9-Deoxy-delta12-PGD2,1TMS,isomer #3CCCCC[C@H](O)C/C=C1/C(O[Si](C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O2873.7Semi standard non polar33892256
9-Deoxy-delta12-PGD2,2TMS,isomer #1CCCCC[C@@H](C/C=C1/C(=O)CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C2782.0Semi standard non polar33892256
9-Deoxy-delta12-PGD2,2TMS,isomer #2CCCCC[C@@H](C/C=C1/C(O[Si](C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C2869.1Semi standard non polar33892256
9-Deoxy-delta12-PGD2,2TMS,isomer #3CCCCC[C@H](O)C/C=C1/C(O[Si](C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C2826.8Semi standard non polar33892256
9-Deoxy-delta12-PGD2,3TMS,isomer #1CCCCC[C@@H](C/C=C1/C(O[Si](C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C2853.4Semi standard non polar33892256
9-Deoxy-delta12-PGD2,3TMS,isomer #1CCCCC[C@@H](C/C=C1/C(O[Si](C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C2763.8Standard non polar33892256
9-Deoxy-delta12-PGD2,3TMS,isomer #1CCCCC[C@@H](C/C=C1/C(O[Si](C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C)O[Si](C)(C)C3136.7Standard polar33892256
9-Deoxy-delta12-PGD2,1TBDMS,isomer #1CCCCC[C@@H](C/C=C1/C(=O)CC[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C(C)(C)C3019.8Semi standard non polar33892256
9-Deoxy-delta12-PGD2,1TBDMS,isomer #2CCCCC[C@H](O)C/C=C1/C(=O)CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C2993.2Semi standard non polar33892256
9-Deoxy-delta12-PGD2,1TBDMS,isomer #3CCCCC[C@H](O)C/C=C1/C(O[Si](C)(C)C(C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O3102.4Semi standard non polar33892256
9-Deoxy-delta12-PGD2,2TBDMS,isomer #1CCCCC[C@@H](C/C=C1/C(=O)CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C3248.9Semi standard non polar33892256
9-Deoxy-delta12-PGD2,2TBDMS,isomer #2CCCCC[C@@H](C/C=C1/C(O[Si](C)(C)C(C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O)O[Si](C)(C)C(C)(C)C3302.2Semi standard non polar33892256
9-Deoxy-delta12-PGD2,2TBDMS,isomer #3CCCCC[C@H](O)C/C=C1/C(O[Si](C)(C)C(C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C3308.1Semi standard non polar33892256
9-Deoxy-delta12-PGD2,3TBDMS,isomer #1CCCCC[C@@H](C/C=C1/C(O[Si](C)(C)C(C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C3540.7Semi standard non polar33892256
9-Deoxy-delta12-PGD2,3TBDMS,isomer #1CCCCC[C@@H](C/C=C1/C(O[Si](C)(C)C(C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C3142.4Standard non polar33892256
9-Deoxy-delta12-PGD2,3TBDMS,isomer #1CCCCC[C@@H](C/C=C1/C(O[Si](C)(C)C(C)(C)C)=CC[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C3296.4Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 9-Deoxy-delta12-PGD2 GC-MS (Non-derivatized) - 70eV, Positivesplash10-05n3-6492000000-72a812cfa4c1aa83675a2017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9-Deoxy-delta12-PGD2 GC-MS (2 TMS) - 70eV, Positivesplash10-0109-9313300000-42423e8ddba5dad62f152017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 9-Deoxy-delta12-PGD2 GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 10V, Positive-QTOFsplash10-0gb9-0129000000-866c9950f2d67f3ce87a2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 20V, Positive-QTOFsplash10-0q4l-3395000000-148d22c7e22daa18bdce2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 40V, Positive-QTOFsplash10-0a4i-9430000000-1fd655b233204214b0fb2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 10V, Negative-QTOFsplash10-000i-0019000000-af954838d61275b1a6b22017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 20V, Negative-QTOFsplash10-014r-2059000000-07745a169a65b73332902017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 40V, Negative-QTOFsplash10-0a4l-9130000000-3871a6c36cd811b8778b2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 10V, Positive-QTOFsplash10-0uxr-0119000000-8d978b2af4a1bdc02d542021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 20V, Positive-QTOFsplash10-0uxr-9625000000-7a66dc97df93f06161432021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 40V, Positive-QTOFsplash10-0a4i-9600000000-0119fa02ae25cf3eb4cb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 10V, Negative-QTOFsplash10-00kr-0019000000-8a49f6b6de6d55d0dfea2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 20V, Negative-QTOFsplash10-05tr-0196000000-2461a0379b4a79587c8e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 9-Deoxy-delta12-PGD2 40V, Negative-QTOFsplash10-0a4m-9310000000-560056a2abfa4ce3b5182021-10-12Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131769823
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]
  2. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  3. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  4. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  5. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.