Showing metabocard for 1-Deoxy-D-xylulose (BMDB0001292)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 22:43:41 UTC
Update Date2020-04-22 15:07:29 UTC
BMDB IDBMDB0001292
Secondary Accession Numbers
  • BMDB01292
Metabolite Identification
Common Name1-Deoxy-D-xylulose
Description1-Deoxy-D-xylulose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 1-Deoxy-D-xylulose exists in all living organisms, ranging from bacteria to humans. Based on a literature review a significant number of articles have been published on 1-Deoxy-D-xylulose.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
1-Deoxy-xyluloseHMDB
Chemical FormulaC5H10O4
Average Molecular Weight134.1305
Monoisotopic Molecular Weight134.057908808
IUPAC Name(2S,3S,4R)-2-(hydroxymethyl)oxolane-3,4-diol
Traditional Name1-deoxy-xylulose
CAS Registry NumberNot Available
SMILES
OC[C@@H]1OC[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2/t3-,4+,5+/m1/s1
InChI KeyKZVAAIRBJJYZOW-WISUUJSJSA-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
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Ether
  • Dialkyl ether
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2ALOGPS
logP-1.9ChemAxon
logS0.89ALOGPS
pKa (Strongest Acidic)12.88ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.92 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.93 m³·mol⁻¹ChemAxon
Polarizability12.64 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-9200000000-bc8cd8af91e7c9a197a1View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0uds-4291000000-59ca220656793d44d9b7View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-1900000000-7090a6712cf92fc92b47View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014r-3900000000-1e02762bd5d3754a4e36View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052b-9000000000-88975f87661b595c76bdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-0900000000-e0e5e2d68edb8bbc84f0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00lr-2900000000-ff5858ced75ca8f420e2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-f94dc6ccbc9cbdbfeed6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f89-4900000000-8a6afa76074a3daf9196View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4l-9200000000-149f3dceb4c97219beb6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9000000000-3ec198bd54c97fa0e89cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0ap1-9400000000-9a51cae153c12e261a4dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4j-9000000000-1ce0654ed02bead3e749View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0005-9000000000-78c20bbe447917d1f4b6View in MoNA
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001292
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022537
KNApSAcK IDC00007292
Chemspider ID17216098
KEGG Compound IDC06257
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6138
PubChem Compound12444984
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceBackstrom, Allyson D.; Austin, R.; McMordie Austin S.; Begley, Tadhg P. A new synthesis of 1-deoxy-D-threo-2-pentulose, a biosynthetic precursor to the thiazole moiety of thiamin. Journal of Carbohydrate Chemistry (1995), 14(1), 171-5.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available