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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-11 17:33:42 UTC
Update Date2021-09-14 15:19:34 UTC
HMDB IDHMDB0029942
Secondary Accession Numbers
  • HMDB29942
Metabolite Identification
Common NameD-Arabinose
DescriptionD-Arabinose (CAS: 10323-20-3) belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Outside of the human body, D-arabinose has been detected, but not quantified in, sweet basils and tamarinds. This could make D-arabinose a potential biomarker for the consumption of these foods.
Structure
Data?1594234757
Synonyms
ValueSource
b-D-ArabinopyranoseGenerator
β-D-ArabinopyranoseGenerator
ArabinopyranoseHMDB
ArabinoseHMDB
D-ArabinopyranoseHMDB
D-ArabinoseHMDB
PectinoseHMDB
beta-D-ArabinopyranoseHMDB
beta-D-ArabinoseHMDB
β-D-ArabinoseHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.13
Monoisotopic Molecular Weight150.052823422
IUPAC Name(3S,4R,5R)-oxane-2,3,4,5-tetrol
Traditional NameD-arabinopyranose
CAS Registry Number6748-95-4
SMILES
O[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4+,5-/m1/s1
InChI KeySRBFZHDQGSBBOR-SQOUGZDYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Oxane
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility380 g/LALOGPS
logP-2.6ALOGPS
logP-2.3ChemAxon
logS0.91ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.42 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Collision Cross Sections

NameAdductTypeData SourceValueReference

Retention Indices

Underivatized

Not Available

Derivatized

DerivativeValueReference
D-Arabinose,1TMS,#11494.4054https://arxiv.org/abs/1905.12712
D-Arabinose,1TMS,#21456.1238https://arxiv.org/abs/1905.12712
D-Arabinose,1TMS,#31492.7703https://arxiv.org/abs/1905.12712
D-Arabinose,1TMS,#41500.9941https://arxiv.org/abs/1905.12712
D-Arabinose,2TMS,#11519.0747https://arxiv.org/abs/1905.12712
D-Arabinose,2TMS,#21515.8954https://arxiv.org/abs/1905.12712
D-Arabinose,2TMS,#31471.6167https://arxiv.org/abs/1905.12712
D-Arabinose,2TMS,#41518.4132https://arxiv.org/abs/1905.12712
D-Arabinose,2TMS,#51477.6942https://arxiv.org/abs/1905.12712
D-Arabinose,2TMS,#61495.9204https://arxiv.org/abs/1905.12712
D-Arabinose,3TMS,#11560.8877https://arxiv.org/abs/1905.12712
D-Arabinose,3TMS,#21548.4874https://arxiv.org/abs/1905.12712
D-Arabinose,3TMS,#31553.7686https://arxiv.org/abs/1905.12712
D-Arabinose,3TMS,#41576.0437https://arxiv.org/abs/1905.12712
D-Arabinose,4TMS,#11645.414https://arxiv.org/abs/1905.12712
D-Arabinose,1TBDMS,#11744.4827https://arxiv.org/abs/1905.12712
D-Arabinose,1TBDMS,#21707.134https://arxiv.org/abs/1905.12712
D-Arabinose,1TBDMS,#31726.6796https://arxiv.org/abs/1905.12712
D-Arabinose,1TBDMS,#41732.7551https://arxiv.org/abs/1905.12712
D-Arabinose,2TBDMS,#11990.6764https://arxiv.org/abs/1905.12712
D-Arabinose,2TBDMS,#21979.0387https://arxiv.org/abs/1905.12712
D-Arabinose,2TBDMS,#31956.1959https://arxiv.org/abs/1905.12712
D-Arabinose,2TBDMS,#41976.0071https://arxiv.org/abs/1905.12712
D-Arabinose,2TBDMS,#51949.6328https://arxiv.org/abs/1905.12712
D-Arabinose,2TBDMS,#61958.3599https://arxiv.org/abs/1905.12712
D-Arabinose,3TBDMS,#12254.8264https://arxiv.org/abs/1905.12712
D-Arabinose,3TBDMS,#22238.8997https://arxiv.org/abs/1905.12712
D-Arabinose,3TBDMS,#32250.2468https://arxiv.org/abs/1905.12712
D-Arabinose,3TBDMS,#42239.2886https://arxiv.org/abs/1905.12712
D-Arabinose,4TBDMS,#12479.7622https://arxiv.org/abs/1905.12712
Spectra

LC-MS/MS

Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-7900000000-524214992b29f1ff9b802021-09-08View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-9000000000-f758a7d33dac04b062752021-09-08View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000000000-4b3e154b12c2ee07bf582021-09-08View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0gc0-1900000000-e784a3fdca89dcb59c122021-09-09View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0m4p-9100000000-fc295e2732f55a0a18c12021-09-09View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0007-9000000000-ba5f29c2c79df8d0956f2021-09-09View Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected and Quantified1041.0984 +/- 657.431 nmol/g wet fecesNot SpecifiedNot Specified
Normal
details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal
details
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB001219
KNApSAcK IDNot Available
Chemspider ID392169
KEGG Compound IDNot Available
BioCyc IDCPD-12049
BiGG IDNot Available
Wikipedia LinkArabinose
METLIN IDNot Available
PubChem Compound444173
PDB IDNot Available
ChEBI ID46996
Food Biomarker OntologyNot Available
VMH IDARAB_D
MarkerDB 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.. .