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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-11 17:33:42 UTC
Update Date2022-03-07 02:52:22 UTC
HMDB IDHMDB0029942
Secondary Accession Numbers
  • HMDB29942
Metabolite Identification
Common NameD-Arabinose
DescriptionD-Arabinose, also known as arabinopyranose or pectinose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Arabinose is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on D-Arabinose.
Structure
Data?1594234757
Synonyms
ValueSource
WURCS=2.0/1,1,0/[a122h-1b_1-5]/1/ChEBI
b-D-ArabinopyranoseHMDB
Β-D-arabinopyranoseHMDB
ArabinopyranoseHMDB
ArabinoseHMDB
D-ArabinopyranoseHMDB
PectinoseHMDB
beta-D-ArabinopyranoseHMDB
beta-D-ArabinoseHMDB
Β-D-arabinoseHMDB
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

Biological location

Source

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 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 Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+134.60130932474
DeepCCS[M-H]-132.37930932474
DeepCCS[M-2H]-166.98230932474
DeepCCS[M+Na]+141.12430932474
AllCCS[M+H]+134.232859911
AllCCS[M+H-H2O]+129.632859911
AllCCS[M+NH4]+138.432859911
AllCCS[M+Na]+139.732859911
AllCCS[M-H]-124.832859911
AllCCS[M+Na-2H]-126.532859911
AllCCS[M+HCOO]-128.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
D-ArabinoseO[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O3000.0Standard polar33892256
D-ArabinoseO[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O1530.6Standard non polar33892256
D-ArabinoseO[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O1384.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
D-Arabinose,1TMS,isomer #1C[Si](C)(C)O[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O1494.4Semi standard non polar33892256
D-Arabinose,1TMS,isomer #2C[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O1456.1Semi standard non polar33892256
D-Arabinose,1TMS,isomer #3C[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O)[C@H]1O1492.8Semi standard non polar33892256
D-Arabinose,1TMS,isomer #4C[Si](C)(C)O[C@H]1[C@H](O)[C@H](O)OC[C@H]1O1501.0Semi standard non polar33892256
D-Arabinose,2TMS,isomer #1C[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H](O)[C@@H]1O1519.1Semi standard non polar33892256
D-Arabinose,2TMS,isomer #2C[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O[Si](C)(C)C)[C@H]1O1515.9Semi standard non polar33892256
D-Arabinose,2TMS,isomer #3C[Si](C)(C)O[C@H]1[C@H](O)[C@H](O)OC[C@H]1O[Si](C)(C)C1471.6Semi standard non polar33892256
D-Arabinose,2TMS,isomer #4C[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O[Si](C)(C)C)[C@@H]1O1518.4Semi standard non polar33892256
D-Arabinose,2TMS,isomer #5C[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O[Si](C)(C)C1477.7Semi standard non polar33892256
D-Arabinose,2TMS,isomer #6C[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O)[C@H]1O[Si](C)(C)C1495.9Semi standard non polar33892256
D-Arabinose,3TMS,isomer #1C[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O1560.9Semi standard non polar33892256
D-Arabinose,3TMS,isomer #2C[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C1548.5Semi standard non polar33892256
D-Arabinose,3TMS,isomer #3C[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C1553.8Semi standard non polar33892256
D-Arabinose,3TMS,isomer #4C[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1576.0Semi standard non polar33892256
D-Arabinose,4TMS,isomer #1C[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1645.4Semi standard non polar33892256
D-Arabinose,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@@H](O)[C@@H](O)[C@@H]1O1744.5Semi standard non polar33892256
D-Arabinose,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O1707.1Semi standard non polar33892256
D-Arabinose,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O)[C@H]1O1726.7Semi standard non polar33892256
D-Arabinose,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@H](O)OC[C@H]1O1732.8Semi standard non polar33892256
D-Arabinose,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O1990.7Semi standard non polar33892256
D-Arabinose,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O1979.0Semi standard non polar33892256
D-Arabinose,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)[C@H](O)OC[C@H]1O[Si](C)(C)C(C)(C)C1956.2Semi standard non polar33892256
D-Arabinose,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O1976.0Semi standard non polar33892256
D-Arabinose,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C1949.6Semi standard non polar33892256
D-Arabinose,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O)[C@H]1O[Si](C)(C)C(C)(C)C1958.4Semi standard non polar33892256
D-Arabinose,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2254.8Semi standard non polar33892256
D-Arabinose,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2238.9Semi standard non polar33892256
D-Arabinose,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](O)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C2250.2Semi standard non polar33892256
D-Arabinose,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2239.3Semi standard non polar33892256
D-Arabinose,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)O[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2479.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - D-Arabinose GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Arabinose 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 - D-Arabinose 10V, Negative-QTOFsplash10-0002-7900000000-524214992b29f1ff9b802021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Arabinose 20V, Negative-QTOFsplash10-0a4i-9000000000-f758a7d33dac04b062752021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Arabinose 40V, Negative-QTOFsplash10-0a4l-9000000000-4b3e154b12c2ee07bf582021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Arabinose 10V, Positive-QTOFsplash10-0gc0-1900000000-e784a3fdca89dcb59c122021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Arabinose 20V, Positive-QTOFsplash10-0m4p-9100000000-fc295e2732f55a0a18c12021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Arabinose 40V, Positive-QTOFsplash10-0007-9000000000-ba5f29c2c79df8d0956f2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView 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 IDC00001115
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
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.. .