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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-03-16 03:42:10 UTC
Update Date2022-03-07 03:17:52 UTC
HMDB IDHMDB0062298
Secondary Accession Numbers
  • HMDB62298
Metabolite Identification
Common Name15-deoxy-PGD2
Description15-deoxy-PGD2 is classified as a member of the Prostaglandins and related compounds. Prostaglandins and related compounds 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. 15-deoxy-PGD2 is considered to be practically insoluble (in water) and acidic. 15-deoxy-PGD2 is an eicosanoid lipid molecule
Structure
Data?1563866292
Synonyms
ValueSource
15-Deoxy-δ-12,14-PGD2Generator
Chemical FormulaC20H30O4
Average Molecular Weight334.456
Monoisotopic Molecular Weight334.214409446
IUPAC Name(5Z)-7-[(1R,2E,5S)-5-hydroxy-2-[(2E)-oct-2-en-1-ylidene]-3-oxocyclopentyl]hept-5-enoic acid
Traditional Name15-deoxy-delta-12,14-PGD2
CAS Registry NumberNot Available
SMILES
[H]\C(CCCC(O)=O)=C(/[H])C[C@]1([H])\C(=C(\[H])/C(/[H])=C(\[H])CCCCC)C(=O)C[C@]1([H])O
InChI Identifier
InChI=1S/C20H30O4/c1-2-3-4-5-6-9-12-16-17(19(22)15-18(16)21)13-10-7-8-11-14-20(23)24/h6-7,9-10,12,17,19,22H,2-5,8,11,13-15H2,1H3,(H,23,24)/b9-6+,10-7-,16-12+/t17-,19+/m1/s1
InChI KeyQUGBPWLPAUHDTI-PLGLXCLHSA-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
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.026 g/lALOGPS
LogP4.34ALOGPS
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP4.34ALOGPS
logP4.31ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)4.38ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity98.8 m³·mol⁻¹ChemAxon
Polarizability39.15 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]+186.93830932474
DeepCCS[M-H]-184.82230932474
DeepCCS[M-2H]-218.22630932474
DeepCCS[M+Na]+192.67830932474
AllCCS[M+H]+188.332859911
AllCCS[M+H-H2O]+185.532859911
AllCCS[M+NH4]+190.932859911
AllCCS[M+Na]+191.632859911
AllCCS[M-H]-188.132859911
AllCCS[M+Na-2H]-189.432859911
AllCCS[M+HCOO]-191.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
15-deoxy-PGD2[H]\C(CCCC(O)=O)=C(/[H])C[C@]1([H])\C(=C(\[H])/C(/[H])=C(\[H])CCCCC)C(=O)C[C@]1([H])O4298.8Standard polar33892256
15-deoxy-PGD2[H]\C(CCCC(O)=O)=C(/[H])C[C@]1([H])\C(=C(\[H])/C(/[H])=C(\[H])CCCCC)C(=O)C[C@]1([H])O2538.3Standard non polar33892256
15-deoxy-PGD2[H]\C(CCCC(O)=O)=C(/[H])C[C@]1([H])\C(=C(\[H])/C(/[H])=C(\[H])CCCCC)C(=O)C[C@]1([H])O2754.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
15-deoxy-PGD2,1TMS,isomer #1CCCCC/C=C/C=C1/C(=O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C2825.5Semi standard non polar33892256
15-deoxy-PGD2,1TMS,isomer #2CCCCC/C=C/C=C1/C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O2787.6Semi standard non polar33892256
15-deoxy-PGD2,1TMS,isomer #3CCCCC/C=C/C=C1/C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O2839.4Semi standard non polar33892256
15-deoxy-PGD2,2TMS,isomer #1CCCCC/C=C/C=C1/C(=O)C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C2761.0Semi standard non polar33892256
15-deoxy-PGD2,2TMS,isomer #2CCCCC/C=C/C=C1/C(O[Si](C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C2794.9Semi standard non polar33892256
15-deoxy-PGD2,2TMS,isomer #3CCCCC/C=C/C=C1/C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O2837.7Semi standard non polar33892256
15-deoxy-PGD2,3TMS,isomer #1CCCCC/C=C/C=C1/C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C2803.2Semi standard non polar33892256
15-deoxy-PGD2,3TMS,isomer #1CCCCC/C=C/C=C1/C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C2719.2Standard non polar33892256
15-deoxy-PGD2,3TMS,isomer #1CCCCC/C=C/C=C1/C(O[Si](C)(C)C)=C[C@H](O[Si](C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C2946.4Standard polar33892256
15-deoxy-PGD2,1TBDMS,isomer #1CCCCC/C=C/C=C1/C(=O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C3055.3Semi standard non polar33892256
15-deoxy-PGD2,1TBDMS,isomer #2CCCCC/C=C/C=C1/C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O3004.2Semi standard non polar33892256
15-deoxy-PGD2,1TBDMS,isomer #3CCCCC/C=C/C=C1/C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O3063.3Semi standard non polar33892256
15-deoxy-PGD2,2TBDMS,isomer #1CCCCC/C=C/C=C1/C(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C3231.9Semi standard non polar33892256
15-deoxy-PGD2,2TBDMS,isomer #2CCCCC/C=C/C=C1/C(O[Si](C)(C)C(C)(C)C)=C[C@H](O)[C@@H]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C3277.5Semi standard non polar33892256
15-deoxy-PGD2,2TBDMS,isomer #3CCCCC/C=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]1C/C=C\CCCC(=O)O3298.0Semi standard non polar33892256
15-deoxy-PGD2,3TBDMS,isomer #1CCCCC/C=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]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C3509.5Semi standard non polar33892256
15-deoxy-PGD2,3TBDMS,isomer #1CCCCC/C=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]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C3180.4Standard non polar33892256
15-deoxy-PGD2,3TBDMS,isomer #1CCCCC/C=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]1C/C=C\CCCC(=O)O[Si](C)(C)C(C)(C)C3119.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 15-deoxy-PGD2 GC-MS (Non-derivatized) - 70eV, Positivesplash10-014l-5392000000-4b6d6783c35d21aa41192017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 15-deoxy-PGD2 GC-MS (2 TMS) - 70eV, Positivesplash10-020r-9215500000-448c1d365df3538f4f2e2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 15-deoxy-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 - 15-deoxy-PGD2 10V, Positive-QTOFsplash10-014j-0169000000-5b00b6cbc44313cdba8d2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 20V, Positive-QTOFsplash10-0avs-2292000000-340f34894155eb581e4c2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 40V, Positive-QTOFsplash10-014l-9200000000-f22e3057dec8bacd839d2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 10V, Negative-QTOFsplash10-001i-0019000000-97f54b4757fa318089eb2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 20V, Negative-QTOFsplash10-0159-1189000000-b133b2e2c83df300f2622017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 40V, Negative-QTOFsplash10-0a4i-9530000000-6c2dca65789786c482f22017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 10V, Positive-QTOFsplash10-014s-1189000000-f3e8af4a0b533d3cf42e2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 20V, Positive-QTOFsplash10-0kwe-5491000000-c90457972951001b4f5b2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 40V, Positive-QTOFsplash10-069u-9200000000-958da6ddee9f2f0db5082021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 10V, Negative-QTOFsplash10-00lr-0009000000-32e689b3c409c1aa30f62021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 20V, Negative-QTOFsplash10-001i-1197000000-f6bb24aed82db67345c02021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 15-deoxy-PGD2 40V, Negative-QTOFsplash10-02td-9362000000-10d999e1a59eb408c19d2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 Compound5283052
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDCE5304
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. 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 ]
  3. 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 ]
  4. 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 ]
  5. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.