Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:35 UTC
HMDB IDHMDB0001292
Secondary Accession Numbers
  • HMDB01292
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. 1-Deoxy-D-xylulose has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 1-deoxy-D-xylulose a potential biomarker for the consumption of these foods. 1-Deoxy-D-xylulose 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 a significant number of articles have been published on 1-Deoxy-D-xylulose.
Structure
Data?1676999735
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
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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 Solubility1050 g/LALOGPS
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 FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+129.04431661259
DarkChem[M-H]-127.17931661259
AllCCS[M+H]+130.74832859911
AllCCS[M-H]-123.64132859911
DeepCCS[M+H]+130.07430932474
DeepCCS[M-H]-127.9430932474
DeepCCS[M-2H]-162.87330932474
DeepCCS[M+Na]+137.15530932474
AllCCS[M+H]+130.732859911
AllCCS[M+H-H2O]+126.132859911
AllCCS[M+NH4]+135.132859911
AllCCS[M+Na]+136.332859911
AllCCS[M-H]-123.632859911
AllCCS[M+Na-2H]-125.732859911
AllCCS[M+HCOO]-128.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-Deoxy-D-xyluloseOC[C@@H]1OC[C@@H](O)[C@@H]1O2636.2Standard polar33892256
1-Deoxy-D-xyluloseOC[C@@H]1OC[C@@H](O)[C@@H]1O1316.4Standard non polar33892256
1-Deoxy-D-xyluloseOC[C@@H]1OC[C@@H](O)[C@@H]1O1288.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
1-Deoxy-D-xylulose,1TMS,isomer #1C[Si](C)(C)OC[C@@H]1OC[C@@H](O)[C@@H]1O1349.4Semi standard non polar33892256
1-Deoxy-D-xylulose,1TMS,isomer #2C[Si](C)(C)O[C@@H]1CO[C@@H](CO)[C@H]1O1381.9Semi standard non polar33892256
1-Deoxy-D-xylulose,1TMS,isomer #3C[Si](C)(C)O[C@@H]1[C@H](CO)OC[C@H]1O1374.0Semi standard non polar33892256
1-Deoxy-D-xylulose,2TMS,isomer #1C[Si](C)(C)OC[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H]1O1458.8Semi standard non polar33892256
1-Deoxy-D-xylulose,2TMS,isomer #2C[Si](C)(C)OC[C@@H]1OC[C@@H](O)[C@@H]1O[Si](C)(C)C1458.2Semi standard non polar33892256
1-Deoxy-D-xylulose,2TMS,isomer #3C[Si](C)(C)O[C@@H]1CO[C@@H](CO)[C@H]1O[Si](C)(C)C1445.7Semi standard non polar33892256
1-Deoxy-D-xylulose,3TMS,isomer #1C[Si](C)(C)OC[C@@H]1OC[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1539.1Semi standard non polar33892256
1-Deoxy-D-xylulose,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H]1OC[C@@H](O)[C@@H]1O1575.5Semi standard non polar33892256
1-Deoxy-D-xylulose,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@@H](CO)[C@H]1O1586.0Semi standard non polar33892256
1-Deoxy-D-xylulose,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H]1[C@H](CO)OC[C@H]1O1595.0Semi standard non polar33892256
1-Deoxy-D-xylulose,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O1884.0Semi standard non polar33892256
1-Deoxy-D-xylulose,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H]1OC[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C1890.4Semi standard non polar33892256
1-Deoxy-D-xylulose,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H]1CO[C@@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C1889.7Semi standard non polar33892256
1-Deoxy-D-xylulose,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H]1OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2182.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1-Deoxy-D-xylulose GC-MS (Non-derivatized) - 70eV, Positivesplash10-00di-9200000000-bc8cd8af91e7c9a197a12017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Deoxy-D-xylulose GC-MS (3 TMS) - 70eV, Positivesplash10-0uds-4291000000-59ca220656793d44d9b72017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Deoxy-D-xylulose 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 - 1-Deoxy-D-xylulose 10V, Positive-QTOFsplash10-000i-1900000000-7090a6712cf92fc92b472015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 20V, Positive-QTOFsplash10-014r-3900000000-1e02762bd5d3754a4e362015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 40V, Positive-QTOFsplash10-052b-9000000000-88975f87661b595c76bd2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 10V, Negative-QTOFsplash10-001i-0900000000-e0e5e2d68edb8bbc84f02015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 20V, Negative-QTOFsplash10-00lr-2900000000-ff5858ced75ca8f420e22015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 40V, Negative-QTOFsplash10-0006-9200000000-f94dc6ccbc9cbdbfeed62015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 10V, Negative-QTOFsplash10-0f89-4900000000-8a6afa76074a3daf91962021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 20V, Negative-QTOFsplash10-0a4l-9200000000-149f3dceb4c97219beb62021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 40V, Negative-QTOFsplash10-052f-9000000000-3ec198bd54c97fa0e89c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 10V, Positive-QTOFsplash10-0ap1-9400000000-9a51cae153c12e261a4d2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 20V, Positive-QTOFsplash10-0a4j-9000000000-1ce0654ed02bead3e7492021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Deoxy-D-xylulose 40V, Positive-QTOFsplash10-0005-9000000000-78c20bbe447917d1f4b62021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
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 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
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents 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