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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:41:37 UTC
Update Date2021-09-14 15:45:22 UTC
HMDB IDHMDB0033919
Secondary Accession Numbers
  • HMDB33919
Metabolite Identification
Common Name2-Deoxy-D-ribitol
Description2-Deoxy-D-ribitol 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). 2-Deoxy-D-ribitol has been detected, but not quantified in, herbs and spices. This could make 2-deoxy-D-ribitol a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 2-Deoxy-D-ribitol.
Structure
Data?1563862481
SynonymsNot Available
Chemical FormulaC5H12O4
Average Molecular Weight136.1464
Monoisotopic Molecular Weight136.073558872
IUPAC Namepentane-1,2,3,5-tetrol
Traditional Namepentane-1,2,3,5-tetrol
CAS Registry NumberNot Available
SMILES
OCCC(O)C(O)CO
InChI Identifier
InChI=1S/C5H12O4/c6-2-1-4(8)5(9)3-7/h4-9H,1-3H2
InChI KeyZDAWZDFBPUUDAY-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
Disposition

Biological location

Source

Route of exposure

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 Solubility669 g/LALOGPS
logP10(-2) g/LALOGPS
logP10(-2.4) g/LChemAxon
logS10(0.69) g/LALOGPS
pKa (Strongest Acidic)13.32ChemAxon
pKa (Strongest Basic)-2.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area80.92 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.34 m³·mol⁻¹ChemAxon
Polarizability13.57 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]+128.75431661259
DarkChem[M-H]-122.72331661259
DeepCCS[M+H]+128.04930932474
DeepCCS[M-H]-125.33330932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Deoxy-D-ribitolOCCC(O)C(O)CO2788.6Standard polar33892256
2-Deoxy-D-ribitolOCCC(O)C(O)CO1452.1Standard non polar33892256
2-Deoxy-D-ribitolOCCC(O)C(O)CO1411.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Deoxy-D-ribitol,1TMS,isomer #1C[Si](C)(C)OCCC(O)C(O)CO1445.3Semi standard non polar33892256
2-Deoxy-D-ribitol,1TMS,isomer #2C[Si](C)(C)OC(CCO)C(O)CO1428.5Semi standard non polar33892256
2-Deoxy-D-ribitol,1TMS,isomer #3C[Si](C)(C)OC(CO)C(O)CCO1437.1Semi standard non polar33892256
2-Deoxy-D-ribitol,1TMS,isomer #4C[Si](C)(C)OCC(O)C(O)CCO1439.1Semi standard non polar33892256
2-Deoxy-D-ribitol,2TMS,isomer #1C[Si](C)(C)OCCC(O[Si](C)(C)C)C(O)CO1512.4Semi standard non polar33892256
2-Deoxy-D-ribitol,2TMS,isomer #2C[Si](C)(C)OCCC(O)C(CO)O[Si](C)(C)C1539.5Semi standard non polar33892256
2-Deoxy-D-ribitol,2TMS,isomer #3C[Si](C)(C)OCCC(O)C(O)CO[Si](C)(C)C1552.9Semi standard non polar33892256
2-Deoxy-D-ribitol,2TMS,isomer #4C[Si](C)(C)OC(CO)C(CCO)O[Si](C)(C)C1508.1Semi standard non polar33892256
2-Deoxy-D-ribitol,2TMS,isomer #5C[Si](C)(C)OCC(O)C(CCO)O[Si](C)(C)C1529.7Semi standard non polar33892256
2-Deoxy-D-ribitol,2TMS,isomer #6C[Si](C)(C)OCC(O[Si](C)(C)C)C(O)CCO1532.9Semi standard non polar33892256
2-Deoxy-D-ribitol,3TMS,isomer #1C[Si](C)(C)OCCC(O[Si](C)(C)C)C(CO)O[Si](C)(C)C1582.7Semi standard non polar33892256
2-Deoxy-D-ribitol,3TMS,isomer #2C[Si](C)(C)OCCC(O[Si](C)(C)C)C(O)CO[Si](C)(C)C1588.1Semi standard non polar33892256
2-Deoxy-D-ribitol,3TMS,isomer #3C[Si](C)(C)OCCC(O)C(CO[Si](C)(C)C)O[Si](C)(C)C1606.9Semi standard non polar33892256
2-Deoxy-D-ribitol,3TMS,isomer #4C[Si](C)(C)OCC(O[Si](C)(C)C)C(CCO)O[Si](C)(C)C1575.0Semi standard non polar33892256
2-Deoxy-D-ribitol,4TMS,isomer #1C[Si](C)(C)OCCC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O[Si](C)(C)C1588.6Semi standard non polar33892256
2-Deoxy-D-ribitol,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCCC(O)C(O)CO1686.7Semi standard non polar33892256
2-Deoxy-D-ribitol,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(CCO)C(O)CO1672.1Semi standard non polar33892256
2-Deoxy-D-ribitol,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC(CO)C(O)CCO1672.4Semi standard non polar33892256
2-Deoxy-D-ribitol,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)OCC(O)C(O)CCO1666.5Semi standard non polar33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCCC(O[Si](C)(C)C(C)(C)C)C(O)CO1967.1Semi standard non polar33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCCC(O)C(CO)O[Si](C)(C)C(C)(C)C1967.0Semi standard non polar33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OCCC(O)C(O)CO[Si](C)(C)C(C)(C)C1976.7Semi standard non polar33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(CO)C(CCO)O[Si](C)(C)C(C)(C)C1953.2Semi standard non polar33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)OCC(O)C(CCO)O[Si](C)(C)C(C)(C)C1961.3Semi standard non polar33892256
2-Deoxy-D-ribitol,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(O)CCO1964.9Semi standard non polar33892256
2-Deoxy-D-ribitol,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCCC(O[Si](C)(C)C(C)(C)C)C(CO)O[Si](C)(C)C(C)(C)C2202.3Semi standard non polar33892256
2-Deoxy-D-ribitol,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OCCC(O[Si](C)(C)C(C)(C)C)C(O)CO[Si](C)(C)C(C)(C)C2209.1Semi standard non polar33892256
2-Deoxy-D-ribitol,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OCCC(O)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2215.2Semi standard non polar33892256
2-Deoxy-D-ribitol,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CCO)O[Si](C)(C)C(C)(C)C2197.0Semi standard non polar33892256
2-Deoxy-D-ribitol,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OCCC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2423.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxy-D-ribitol GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9000000000-839920e63ae81833c8432017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxy-D-ribitol GC-MS (4 TMS) - 70eV, Positivesplash10-0a4r-8239400000-e124927e21f7d46072cc2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxy-D-ribitol 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-Deoxy-D-ribitol 10V, Positive-QTOFsplash10-014r-1900000000-1d6f0c49719625480ec02015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 20V, Positive-QTOFsplash10-0002-9400000000-930d72de6d5f26e844ff2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 40V, Positive-QTOFsplash10-0pba-9200000000-cfcf887fe98d3efc39ae2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 10V, Negative-QTOFsplash10-000i-3900000000-2700ddc4f5cfbb58b2702015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 20V, Negative-QTOFsplash10-0551-9300000000-9cbfd49729ae70e723c72015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 40V, Negative-QTOFsplash10-0abm-9000000000-2c75d0978b923b706f822015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 10V, Negative-QTOFsplash10-0a4r-9600000000-27094c8c9dff7a6077d52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 20V, Negative-QTOFsplash10-0a4i-9000000000-7d8d0517d4705455e2572021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 40V, Negative-QTOFsplash10-052f-9000000000-fe53649d05e8056353de2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 10V, Positive-QTOFsplash10-0uxr-7900000000-f1f7bfd37043335b02c12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 20V, Positive-QTOFsplash10-0k92-9300000000-2e0d55e703bfc59cd5da2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxy-D-ribitol 40V, Positive-QTOFsplash10-0005-9000000000-60ddf91bc24f49a7d70c2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart 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 IDFDB012117
KNApSAcK IDC00055565
Chemspider ID218353
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound249377
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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .