5-Keto-D-gluconate (PAMDB000820)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000820
Identification
Name: 5-Keto-D-gluconate
Description:5-Keto-D-gluconate is metabolized from glucose in certain bacterial species. It is an intermediate in L-idonate degradation and ketogluconate metabolism. 5-Keto-D-gluconate 5-reductase catalyzes the reversible reduction of 5-ketogluconate to D-gluconate. This is the second reaction of the L-idonate catabolic pathway after uptake of L-idonate into the cell. The enzyme specifically reduces 5-ketogluconate using either NADH or NADPH. The enzyme is also specific for D-gluconate oxidation using NADP as the coenzyme, NAD does not serve as a coenzyme.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 5-Dehydro-D-gluconate
  • 5-Dehydro-D-gluconic acid
  • 5-Dehydrogluconate
  • 5-Dehydrogluconic acid
  • 5-k-Gluconate
  • 5-k-Gluconic acid
  • 5-Keto-D-gluconate
  • 5-Keto-D-gluconic acid
  • 5-Ketogluconate
  • 5-Ketogluconic acid
  • 5K-Gluconate
  • 5K-Gluconic acid
  • D-tagaturonate
  • D-tagaturonic acid
  • Hex-5-ulosonate
  • Hex-5-ulosonic acid
  • Tagaturonate
  • Tagaturonic acid
Chemical Formula: C6H10O7
Average Molecular Weight: 194.1394
Monoisotopic Molecular Weight: 194.042652674
InChI Key: IZSRJDGCGRAUAR-UHFFFAOYSA-N
InChI:InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h3-5,7,9-11H,1H2,(H,12,13)
CAS number: 3470-36-8
IUPAC Name:(2R,3S,4S)-2,3,4,6-tetrahydroxy-5-oxohexanoic acid
Traditional IUPAC Name: 5-dehydrogluconate
SMILES:OCC(=O)C(O)C(O)C(O)C(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
Kingdom Organic compounds
Super ClassOrganic acids and derivatives
Class Hydroxy acids and derivatives
Sub ClassMedium-chain hydroxy acids and derivatives
Direct Parent Medium-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Beta-hydroxy acid
  • Fatty acyl
  • Fatty acid
  • Monosaccharide
  • Beta-hydroxy ketone
  • Beta-ketoaldehyde
  • Alpha-hydroxy acid
  • Acyloin
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Polyol
  • Ketone
  • 1,2-diol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-1
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility112.0 mg/mLALOGPS
logP-2.5ALOGPS
logP-2.9ChemAxon
logS-0.24ALOGPS
pKa (Strongest Acidic)3.24ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area135.29 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.43 m3·mol-1ChemAxon
Polarizability16.32 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
D-Altronate + NAD <> Hydrogen ion + NADH + 5-Keto-D-gluconate + D-Tagaturonate
D-Galacturonate <> 5-Keto-D-gluconate
2,5-Diketo-D-gluconate + Hydrogen ion + NADH > 5-Keto-D-gluconate + NAD
2,5-Diketo-D-gluconate + Hydrogen ion + NADPH > 5-Keto-D-gluconate + NADP
5-Keto-D-gluconate + Hydrogen ion + NADPH <> Gluconic acid + NADP
5-Keto-D-gluconate + Hydrogen ion + NADH <> D-Galactonate + NAD
5-Keto-D-gluconate + Hydrogen ion + NADPH > D-Galactonate + NADP
D-Altronate + NAD <> 5-Keto-D-gluconate + NADH + Hydrogen ion
NAD(P)<sup>+</sup> + L-Idonate <> NAD(P)H + 5-Keto-D-gluconate + Hydrogen ion
NAD(P)<sup>+</sup> + Gluconic acid <> NAD(P)H + 5-Keto-D-gluconate + Hydrogen ion
L-Idonate + NAD(P)(+) > 5-Keto-D-gluconate + NAD(P)H
Gluconic acid + NAD(P)(+) > 5-Keto-D-gluconate + NAD(P)H
Gluconic acid + NAD + NADP <> 5-Keto-D-gluconate + NADH + NADPH + Hydrogen ion
L-Idonate + NAD + NADP <> 5-Keto-D-gluconate + NADH + NADPH + Hydrogen ion
Pathways:
  • Pentose and glucuronate interconversions pae00040
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004j-2900000000-0af971abb8407c7b640cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-9400000000-31b04757e6b9cbdbd7f9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9100000000-f97908d555d85b4bc6e1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-05n0-9800000000-7c97e2503675894394d0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4r-9400000000-7961255e83b6d2f38bfaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9100000000-b1bbfcb7ec35db5cfe1eView in MoNA
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: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID17426
HMDB IDHMDB11731
Pubchem Compound ID157
Kegg IDC01062
ChemSpider ID152
Wikipedia IDNot Available
BioCyc ID5-DEHYDROGLUCONATE
EcoCyc ID5-DEHYDROGLUCONATE

Enzymes

Protein Details
• Glyoxylate/hydroxypyruvate reductase B
General function:
Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Specific function:
Catalyzes the NADPH-dependent reduction of glyoxylate and hydroxypyruvate into glycolate and glycerate, respectively. Can also reduce 2,5-diketo-D-gluconate (25DKG) to 5-keto-D- gluconate (5KDG), 2-keto-D-gluconate (2KDG) to D-gluconate, and 2- keto-L-gulonate (2KLG) to L-idonate (IA), but it is not its physiological function. Inactive towards 2-oxoglutarate, oxaloacetate, pyruvate, 5-keto-D-gluconate, D-fructose and L- sorbose. Activity with NAD is very low
Gene Name:
ghrB
Locus Tag:
PA2263
Molecular weight:
35.6 kDa
Reactions
Glycolate + NADP(+) = glyoxylate + NADPH.
D-glycerate + NAD(P)(+) = hydroxypyruvate + NAD(P)H.
D-gluconate + NADP(+) = 2-dehydro-D-gluconate + NADPH.

Transporters