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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2013-02-26 19:02:16 UTC
Update Date2022-03-07 03:17:36 UTC
HMDB IDHMDB0059753
Secondary Accession Numbers
  • HMDB59753
Metabolite Identification
Common Name2-Deoxypentonic acid
Description2-Deoxypentonic acid, also known as 2-deoxypentonate, belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. 2-Deoxypentonic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). These are fatty acids in which the chain bears an hydroxyl group.
Structure
Data?1563865970
Synonyms
ValueSource
2-DeoxypentonateGenerator
3,4,5-TrihydroxypentanoateGenerator
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name3,4,5-trihydroxypentanoic acid
Traditional Name3,4,5-trihydroxypentanoic acid
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)CC(O)=O
InChI Identifier
InChI=1S/C5H10O5/c6-2-4(8)3(7)1-5(9)10/h3-4,6-8H,1-2H2,(H,9,10)
InChI KeyVBUWJOHKCBQXNU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassBeta hydroxy acids and derivatives
Direct ParentBeta hydroxy acids and derivatives
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Short-chain hydroxy acid
  • Fatty acid
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Polyol
  • Organooxygen compound
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Primary alcohol
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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 Solubility511 g/LALOGPS
logP-2ALOGPS
logP-2.1ChemAxon
logS0.53ALOGPS
pKa (Strongest Acidic)4.03ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.97 m³·mol⁻¹ChemAxon
Polarizability13.52 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+133.07431661259
DarkChem[M-H]-126.93831661259
DeepCCS[M+H]+128.49130932474
DeepCCS[M-H]-125.43830932474
DeepCCS[M-2H]-161.91530932474
DeepCCS[M+Na]+137.07830932474
AllCCS[M+H]+135.332859911
AllCCS[M+H-H2O]+131.332859911
AllCCS[M+NH4]+139.032859911
AllCCS[M+Na]+140.032859911
AllCCS[M-H]-127.332859911
AllCCS[M+Na-2H]-129.532859911
AllCCS[M+HCOO]-132.032859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Deoxypentonic acidOCC(O)C(O)CC(O)=O3142.2Standard polar33892256
2-Deoxypentonic acidOCC(O)C(O)CC(O)=O1400.1Standard non polar33892256
2-Deoxypentonic acidOCC(O)C(O)CC(O)=O1458.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Deoxypentonic acid,1TMS,isomer #1C[Si](C)(C)OCC(O)C(O)CC(=O)O1547.0Semi standard non polar33892256
2-Deoxypentonic acid,1TMS,isomer #2C[Si](C)(C)OC(CO)C(O)CC(=O)O1556.5Semi standard non polar33892256
2-Deoxypentonic acid,1TMS,isomer #3C[Si](C)(C)OC(CC(=O)O)C(O)CO1520.0Semi standard non polar33892256
2-Deoxypentonic acid,1TMS,isomer #4C[Si](C)(C)OC(=O)CC(O)C(O)CO1539.5Semi standard non polar33892256
2-Deoxypentonic acid,2TMS,isomer #1C[Si](C)(C)OCC(O[Si](C)(C)C)C(O)CC(=O)O1621.3Semi standard non polar33892256
2-Deoxypentonic acid,2TMS,isomer #2C[Si](C)(C)OCC(O)C(CC(=O)O)O[Si](C)(C)C1602.1Semi standard non polar33892256
2-Deoxypentonic acid,2TMS,isomer #3C[Si](C)(C)OCC(O)C(O)CC(=O)O[Si](C)(C)C1598.0Semi standard non polar33892256
2-Deoxypentonic acid,2TMS,isomer #4C[Si](C)(C)OC(CO)C(CC(=O)O)O[Si](C)(C)C1589.2Semi standard non polar33892256
2-Deoxypentonic acid,2TMS,isomer #5C[Si](C)(C)OC(=O)CC(O)C(CO)O[Si](C)(C)C1597.0Semi standard non polar33892256
2-Deoxypentonic acid,2TMS,isomer #6C[Si](C)(C)OC(=O)CC(O[Si](C)(C)C)C(O)CO1551.5Semi standard non polar33892256
2-Deoxypentonic acid,3TMS,isomer #1C[Si](C)(C)OCC(O[Si](C)(C)C)C(CC(=O)O)O[Si](C)(C)C1667.0Semi standard non polar33892256
2-Deoxypentonic acid,3TMS,isomer #2C[Si](C)(C)OCC(O[Si](C)(C)C)C(O)CC(=O)O[Si](C)(C)C1663.5Semi standard non polar33892256
2-Deoxypentonic acid,3TMS,isomer #3C[Si](C)(C)OCC(O)C(CC(=O)O[Si](C)(C)C)O[Si](C)(C)C1648.1Semi standard non polar33892256
2-Deoxypentonic acid,3TMS,isomer #4C[Si](C)(C)OC(=O)CC(O[Si](C)(C)C)C(CO)O[Si](C)(C)C1636.1Semi standard non polar33892256
2-Deoxypentonic acid,4TMS,isomer #1C[Si](C)(C)OCC(O[Si](C)(C)C)C(CC(=O)O[Si](C)(C)C)O[Si](C)(C)C1677.3Semi standard non polar33892256
2-Deoxypentonic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(O)C(O)CC(=O)O1809.2Semi standard non polar33892256
2-Deoxypentonic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(CO)C(O)CC(=O)O1817.9Semi standard non polar33892256
2-Deoxypentonic acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(CC(=O)O)C(O)CO1783.6Semi standard non polar33892256
2-Deoxypentonic acid,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)CC(O)C(O)CO1772.4Semi standard non polar33892256
2-Deoxypentonic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(O)CC(=O)O2103.8Semi standard non polar33892256
2-Deoxypentonic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCC(O)C(CC(=O)O)O[Si](C)(C)C(C)(C)C2068.6Semi standard non polar33892256
2-Deoxypentonic acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OCC(O)C(O)CC(=O)O[Si](C)(C)C(C)(C)C2036.7Semi standard non polar33892256
2-Deoxypentonic acid,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(CO)C(CC(=O)O)O[Si](C)(C)C(C)(C)C2054.7Semi standard non polar33892256
2-Deoxypentonic acid,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)OC(=O)CC(O)C(CO)O[Si](C)(C)C(C)(C)C2032.1Semi standard non polar33892256
2-Deoxypentonic acid,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)OC(=O)CC(O[Si](C)(C)C(C)(C)C)C(O)CO2006.5Semi standard non polar33892256
2-Deoxypentonic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CC(=O)O)O[Si](C)(C)C(C)(C)C2312.4Semi standard non polar33892256
2-Deoxypentonic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(O)CC(=O)O[Si](C)(C)C(C)(C)C2297.4Semi standard non polar33892256
2-Deoxypentonic acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OCC(O)C(CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2280.4Semi standard non polar33892256
2-Deoxypentonic acid,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)CC(O[Si](C)(C)C(C)(C)C)C(CO)O[Si](C)(C)C(C)(C)C2268.7Semi standard non polar33892256
2-Deoxypentonic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2482.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxypentonic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-06sc-9000000000-c78de6841f3acf1fa76b2017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxypentonic acid GC-MS (4 TMS) - 70eV, Positivesplash10-00g0-9027200000-adc32665fe9b412fb0fb2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxypentonic acid 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 - 2-Deoxypentonic acid 10V, Positive-QTOFsplash10-001i-1900000000-abab4e4ee07915ad25df2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 20V, Positive-QTOFsplash10-07cu-9700000000-56ec7d5976e9023705802017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 40V, Positive-QTOFsplash10-06xx-9000000000-cb82a1f13b50d91492bd2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 10V, Negative-QTOFsplash10-052b-3900000000-0b54ad95ab8a0e82a5a02017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 20V, Negative-QTOFsplash10-0a4r-9300000000-1190b2589b795883f41c2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 40V, Negative-QTOFsplash10-0a4l-9000000000-6a9184456a482fb916e12017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 10V, Negative-QTOFsplash10-0a4j-3900000000-a9aa746c80102cdac1262021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 20V, Negative-QTOFsplash10-0a4l-9000000000-9dafbd8baf4cb85faab22021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 40V, Negative-QTOFsplash10-0006-9000000000-01325c407d88a7a206322021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 10V, Positive-QTOFsplash10-00li-7900000000-a34eed2d06f591b7cbbd2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 20V, Positive-QTOFsplash10-00xv-9300000000-8da3691bcbc57bad1a6c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxypentonic acid 40V, Positive-QTOFsplash10-0006-9000000000-7a979d2ff58310d5e57c2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
      Not Available
details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
      Not Available
details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal
      Not Available
details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Female
Normal
      Not Available
details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Female
Normal
      Not Available
details
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 Compound13871872
PDB IDNot Available
ChEBI ID89890
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 ReferencesNot Available