3-Dehydro-2-deoxy-D-gluconate (ECMDB04047) (M2MDB000580)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (1)
Record Information
Version2.0
Creation Date2012-05-31 14:03:22 -0600
Update Date2015-06-03 15:54:40 -0600
Secondary Accession Numbers
  • ECMDB04047
Identification
Name:3-Dehydro-2-deoxy-D-gluconate
Description3-Dehydro-2-deoxy-D-gluconate is an intermediate in pectin degradation and is involved in carbohydrate metabolism as well as pentose and glucuronate interconversions. It is a substrate for the enzyme 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase. This enzyme catalyzes the reduction of 2,5-diketo-3-deoxygluconate (DKII or 4,6-dihydroxy-2,5-dioxohexanoate) into 2-keto-3-deoxygluconate (KDG or 2-dehydro-3-deoxygluconate) with a concomitant oxidation of NADH
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 2-Deoxy-3-dehydro-D-gluconate
  • 2-Deoxy-3-dehydro-D-gluconic acid
  • 2-Deoxy-3-ketogluconate
  • 2-Deoxy-3-ketogluconic acid
  • 2-Deoxy-3-oxogluconate
  • 2-Deoxy-3-oxogluconic acid
  • 3-Dehydro-2-deoxy-D-gluconic acid
  • 3-Dehydro-2-deoxy-gluconate
  • 3-Dehydro-2-deoxy-gluconic acid
  • De-O-K-gluconate
  • De-O-K-gluconic acid
  • Deoxy-ketogluconate
  • Deoxy-ketogluconic acid
Chemical Formula:C6H10O6
Weight:Average: 178.14
Monoisotopic: 178.047738052
InChI Key:CNLFCQPCBQQMHK-UHFFFAOYSA-N
InChI:InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h4,6-7,9,12H,1-2H2,(H,10,11)
CAS number:Not Available
IUPAC Name:4,5,6-trihydroxy-3-oxohexanoic acid
Traditional IUPAC Name:4,5,6-trihydroxy-3-oxohexanoic acid
SMILES:OCC(O)C(O)C(=O)CC(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar acids and derivatives
Alternative Parents
Substituents
  • Hexose monosaccharide
  • Medium-chain keto acid
  • Sugar acid
  • Beta-keto acid
  • Acyloin
  • 1,3-dicarbonyl compound
  • Beta-hydroxy ketone
  • Monosaccharide
  • Keto acid
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • Polyol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Carbonyl group
  • Primary alcohol
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility209 g/LALOGPS
logP-2ALOGPS
logP-1.9ChemAxon
logS0.07ALOGPS
pKa (Strongest Acidic)3.75ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area115.06 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity36.24 m³·mol⁻¹ChemAxon
Polarizability15.51 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
NAD + 2-Deoxygluconate <> Hydrogen ion + NADH + 3-Dehydro-2-deoxy-D-gluconate
2-Deoxygluconate + NAD > 3-Dehydro-2-deoxy-D-gluconate + NADH + Hydrogen ion
SMPDB Pathways:
Collection of Reactions without pathwaysPW001891 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Pentose and glucuronate interconversions ec00040
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-2900000000-642decf396af7b5cc277View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9500000000-1d75fdeb0386f041e732View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-06r6-9100000000-910031343a7cd5b307a3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-066r-6900000000-560ccb74a7e1bb8c5090View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ab9-9300000000-15062933572e0ceb3f15View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0ab9-9000000000-4db43b76044f589b7e8fView 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16622
HMDB IDNot Available
Pubchem Compound ID627
Kegg IDC03926
ChemSpider ID607
Wikipedia IDNot Available
BioCyc IDDE-O-K-GLUCONATE
EcoCyc IDDE-O-K-GLUCONATE

Enzymes

Protein Details
1. 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase
General function:
Involved in 2-deoxy-D-gluconate 3-dehydrogenase activity
Specific function:
Catalyzes the reduction of 2,5-diketo-3-deoxygluconate (DKII or 4,6-dihydroxy-2,5-dioxohexanoate) into 2-keto-3- deoxygluconate (KDG or 2-dehydro-3-deoxygluconate) with a concomitant oxidation of NADH
Gene Name:
kduD
Uniprot ID:
P37769
Molecular weight:
27070
Reactions
2-dehydro-3-deoxy-D-gluconate + NAD(+) = (4S)-4,6-dihydroxy-2,5-dioxohexanoate + NADH.