1-Deoxy-D-xylulose (ECMDB01292) (M2MDB000325)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (1)
Record Information
Version2.0
Creation Date2012-05-31 13:49:11 -0600
Update Date2015-09-13 15:15:22 -0600
Secondary Accession Numbers
  • ECMDB01292
Identification
Name:1-Deoxy-D-xylulose
Description1-deoxy-D-xylulose 5-phosphate serves as a precursor for the biosynthesis of the vitamins thiamine and pyridoxal and for the formation of isopentenyl pyrophosphate and dimethylallyl pyrophosphate via the nonmevalonate pathway of terpenoid biosynthesis. Escherichia coli incorporates unphosphorylated 1-deoxy-D-xylulose into the terpenoid side chain of ubiquinones with high efficacy. D-xylulokinase (EC 2.7.1.17) catalyzes the phosphorylation of 1-deoxy-D-xylulose
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 1-Deoxy-2-pentulose
  • 1-Deoxy-D-threo-2-pentulose
  • 1-Deoxy-D-threo-2-Pentulose (9CI)
  • 1-Deoxy-D-threo-pentulose
  • 1-Deoxy-D-xylulose
  • 1-Deoxy-xylulose
  • D-1-Deoxyxylulose
  • Deoxyxylulose
  • DXylulose
Chemical Formula:C5H10O4
Weight:Average: 134.1305
Monoisotopic: 134.057908808
InChI Key:KZVAAIRBJJYZOW-WISUUJSJSA-N
InChI:InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2/t3-,4+,5+/m1/s1
CAS number:60299-43-6
IUPAC Name:(2S,3S,4R)-2-(hydroxymethyl)oxolane-3,4-diol
Traditional IUPAC Name:1-deoxy-xylulose
SMILES:OC[C@@H]1OC[C@@H](O)[C@@H]1O
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
Physical Properties
State:Solid
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
LogP:-1.19 +/- 0.59PhysProp
Predicted 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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosine triphosphate + 1-Deoxy-D-xylulose > ADP + 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
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 SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Backstrom, 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
External Links:
ResourceLink
CHEBI ID16493
HMDB IDHMDB01292
Pubchem Compound ID12444984
Kegg IDC06257
ChemSpider ID17216098
Wikipedia IDNot Available
BioCyc IDCPD-1093
EcoCyc IDCPD-1093

Enzymes

Protein Details
1. Xylulose kinase
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-xylulose = ADP + D-xylulose 5- phosphate
Gene Name:
xylB
Uniprot ID:
P09099
Molecular weight:
52618
Reactions
ATP + D-xylulose = ADP + D-xylulose 5-phosphate.