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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:41:35 UTC
Update Date2022-03-07 02:52:52 UTC
HMDB IDHMDB0031201
Secondary Accession Numbers
  • HMDB31201
Metabolite Identification
Common Name3-Deoxy-D-arabinitol
Description3-Deoxy-D-arabinitol, also known as 1,2,4,5-pentanetetrol or pentane-1,2,4,5-tetrol, belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl). Based on a literature review very few articles have been published on 3-Deoxy-D-arabinitol.
Structure
Data?1563862094
Synonyms
ValueSource
1,2,4,5-PentanetetrolChEBI
1,2,4,5-TetrahydroxypentaneChEBI
Pentane-1,2,4,5-tetrolChEBI
D-Threo-formHMDB
Chemical FormulaC5H12O4
Average Molecular Weight136.1464
Monoisotopic Molecular Weight136.073558872
IUPAC Namepentane-1,2,4,5-tetrol
Traditional Namepentane-1,2,4,5-tetrol
CAS Registry Number92691-36-6
SMILES
OCC(O)CC(O)CO
InChI Identifier
InChI=1S/C5H12O4/c6-2-4(8)1-5(9)3-7/h4-9H,1-3H2
InChI KeyVHDMXHLHMMROPO-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentSecondary alcohols
Alternative Parents
Substituents
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point102 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility623 g/LALOGPS
logP-2ALOGPS
logP-2.4ChemAxon
logS0.66ALOGPS
pKa (Strongest Acidic)13.91ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area80.92 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.34 m³·mol⁻¹ChemAxon
Polarizability13.55 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]+130.38331661259
DarkChem[M-H]-123.96431661259
DeepCCS[M+H]+129.19230932474
DeepCCS[M-H]-126.37730932474
DeepCCS[M-2H]-163.01630932474
DeepCCS[M+Na]+137.8530932474
AllCCS[M+H]+132.232859911
AllCCS[M+H-H2O]+128.132859911
AllCCS[M+NH4]+136.032859911
AllCCS[M+Na]+137.132859911
AllCCS[M-H]-125.932859911
AllCCS[M+Na-2H]-128.632859911
AllCCS[M+HCOO]-131.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Deoxy-D-arabinitolOCC(O)CC(O)CO2773.1Standard polar33892256
3-Deoxy-D-arabinitolOCC(O)CC(O)CO1456.2Standard non polar33892256
3-Deoxy-D-arabinitolOCC(O)CC(O)CO1362.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Deoxy-D-arabinitol,1TMS,isomer #1C[Si](C)(C)OCC(O)CC(O)CO1464.4Semi standard non polar33892256
3-Deoxy-D-arabinitol,1TMS,isomer #2C[Si](C)(C)OC(CO)CC(O)CO1441.3Semi standard non polar33892256
3-Deoxy-D-arabinitol,2TMS,isomer #1C[Si](C)(C)OCC(CC(O)CO)O[Si](C)(C)C1553.5Semi standard non polar33892256
3-Deoxy-D-arabinitol,2TMS,isomer #2C[Si](C)(C)OCC(O)CC(CO)O[Si](C)(C)C1537.4Semi standard non polar33892256
3-Deoxy-D-arabinitol,2TMS,isomer #3C[Si](C)(C)OCC(O)CC(O)CO[Si](C)(C)C1560.1Semi standard non polar33892256
3-Deoxy-D-arabinitol,2TMS,isomer #4C[Si](C)(C)OC(CO)CC(CO)O[Si](C)(C)C1523.0Semi standard non polar33892256
3-Deoxy-D-arabinitol,3TMS,isomer #1C[Si](C)(C)OCC(CC(CO)O[Si](C)(C)C)O[Si](C)(C)C1579.6Semi standard non polar33892256
3-Deoxy-D-arabinitol,3TMS,isomer #2C[Si](C)(C)OCC(O)CC(CO[Si](C)(C)C)O[Si](C)(C)C1607.5Semi standard non polar33892256
3-Deoxy-D-arabinitol,4TMS,isomer #1C[Si](C)(C)OCC(CC(CO[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C1571.9Semi standard non polar33892256
3-Deoxy-D-arabinitol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(O)CC(O)CO1685.5Semi standard non polar33892256
3-Deoxy-D-arabinitol,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(CO)CC(O)CO1683.6Semi standard non polar33892256
3-Deoxy-D-arabinitol,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(CC(O)CO)O[Si](C)(C)C(C)(C)C1991.4Semi standard non polar33892256
3-Deoxy-D-arabinitol,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCC(O)CC(CO)O[Si](C)(C)C(C)(C)C1964.9Semi standard non polar33892256
3-Deoxy-D-arabinitol,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OCC(O)CC(O)CO[Si](C)(C)C(C)(C)C1968.8Semi standard non polar33892256
3-Deoxy-D-arabinitol,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(CO)CC(CO)O[Si](C)(C)C(C)(C)C1955.5Semi standard non polar33892256
3-Deoxy-D-arabinitol,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(CC(CO)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2200.9Semi standard non polar33892256
3-Deoxy-D-arabinitol,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCC(O)CC(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2213.5Semi standard non polar33892256
3-Deoxy-D-arabinitol,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCC(CC(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2429.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxy-D-arabinitol GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9100000000-928bfa7c5ce9980aebaa2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxy-D-arabinitol GC-MS (4 TMS) - 70eV, Positivesplash10-0ab9-9156300000-d764773252e6d8a2bfe92017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxy-D-arabinitol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Deoxy-D-arabinitol 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 - 3-Deoxy-D-arabinitol 10V, Positive-QTOFsplash10-000i-1900000000-a67e7b5d5675757b71572015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 20V, Positive-QTOFsplash10-0wp0-7900000000-45d77e13624867d894632015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 40V, Positive-QTOFsplash10-0a4i-9200000000-36c46cdb44e02247a93d2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 10V, Negative-QTOFsplash10-000i-3900000000-39821d751f8cb7e7ea262015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 20V, Negative-QTOFsplash10-0a4r-9500000000-e7458a28cff265dfeae22015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 40V, Negative-QTOFsplash10-0a4l-9000000000-919bfcfb099ab021983c2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 10V, Negative-QTOFsplash10-0ap1-7900000000-e78140a9f64a9df0e88a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 20V, Negative-QTOFsplash10-0a4l-9000000000-9408e30e7ba0a9ff7df02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 40V, Negative-QTOFsplash10-0a4l-9000000000-e158a7b6b031088ab30d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 10V, Positive-QTOFsplash10-0uy0-1900000000-add5c4e07fa0684cab2d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 20V, Positive-QTOFsplash10-0pdi-9400000000-ea111471a120a87910142021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 40V, Positive-QTOFsplash10-0pbd-9200000000-28fbb2b9e6412e47843e2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB003222
KNApSAcK IDC00055167
Chemspider ID10619290
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14865845
PDB IDNot Available
ChEBI ID111506
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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .