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5-Dehydro-4-deoxy-D-glucarate (M2MDB000950)

Record Information
Version2.0
Creation Date2012-05-31 14:27:35 -0600
Update Date2015-06-03 17:19:19 -0600
Secondary Accession Numbers
  • ECMDB20102
Identification
Name:5-Dehydro-4-deoxy-D-glucarate
Description5-dehydro-4-deoxy-D-glucarate is a member of the chemical class known as Hexoses. These are monosaccharides in which the sugar unit is a hexose. KDG is invovled in D-glucarate metabolism. Crystals of GlucD have been obtained into which the substrate D-glucarate and two competitive inhibitors, 4-deoxy-D-glucarate and xylarohydroxamate, could be diffused; D-glucarate is converted to the dehydration product, 5-keto-4-deoxy-D-glucarate (KDG). (PMID 10769114)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 2,3-Dihydroxy-5-oxo-hexanedioate
  • 2,3-Dihydroxy-5-oxo-hexanedioic acid
  • 3-deoxy-(L)-threo-2-hexulosarate
  • 3-Deoxy-(L)-threo-2-hexulosarate
  • 3-Deoxy-(L)-threo-2-hexulosaric acid
  • 3-deoxy-L-threo-hex-2-ulosarate
  • 3-Deoxy-L-threo-hex-2-ulosarate
  • 3-Deoxy-L-threo-hex-2-ulosaric acid
  • 5-Dehydro-4-deoxy-D-glucarate
  • 5-Dehydro-4-deoxy-D-glucaric acid
  • 5-KDG
  • 5-Keto-4-deoxy-D-glucarate
  • 5-Keto-4-deoxy-D-glucaric acid
  • GLR
  • KDG
  • KGR
Chemical Formula:C6H8O7
Weight:Average: 192.1235
Monoisotopic: 192.02700261
InChI Key:QUURPCHWPQNNGL-ZAFYKAAXSA-N
InChI:InChI=1S/C6H8O7/c7-2(4(9)6(12)13)1-3(8)5(10)11/h2,4,7,9H,1H2,(H,10,11)(H,12,13)/t2-,4+/m0/s1
CAS number:Not Available
IUPAC Name:(2R,3S)-2,3-dihydroxy-5-oxohexanedioic acid
Traditional IUPAC Name:5-dehydro-4-deoxy-D-glucarate
SMILES:[H][C@](O)(CC(=O)C(O)=O)[C@@]([H])(O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassMedium-chain keto acids and derivatives
Direct ParentMedium-chain keto acids and derivatives
Alternative Parents
Substituents
  • Medium-chain keto acid
  • Beta-hydroxy acid
  • Alpha-hydroxy acid
  • Alpha-keto acid
  • Beta-hydroxy ketone
  • Dicarboxylic acid or derivatives
  • Monosaccharide
  • Hydroxy acid
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • 1,2-diol
  • Ketone
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility52.7 g/LALOGPS
logP-1.2ALOGPS
logP-1.5ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)2.5ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity36.18 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:
Glucaric acid > 5-Dehydro-4-deoxy-D-glucarate + Water
5-Dehydro-4-deoxy-D-glucarate > Tartronate semialdehyde + Pyruvic acid
Galactaric acid > 5-Dehydro-4-deoxy-D-glucarate + Water
D-Glucarate + Glucaric acid <> 5-Dehydro-4-deoxy-D-glucarate + Water
5-Dehydro-4-deoxy-D-glucarate <> Pyruvic acid + Tartronate semialdehyde
D-Galactarate + Galactaric acid <> 5-Dehydro-4-deoxy-D-glucarate + Water
D-glucarate > 5-Dehydro-4-deoxy-D-glucarate + Water
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-1900000000-dc22098bdfbe7bf4390dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-056r-3900000000-d866ef19e96da0564480View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-9400000000-a4c21560ef2a755924c8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-006w-2900000000-670ae8cd92a88762c2afView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fg2-7900000000-1e841b13a298bc87f638View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0udi-9800000000-3d471b650b26cf2a0f96View 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 ID42819
HMDB IDNot Available
Pubchem Compound ID439290
Kegg IDC00679
ChemSpider ID388423
Wikipedia IDNot Available
BioCyc ID5-KETO-4-DEOXY-D-GLUCARATE
EcoCyc ID5-KETO-4-DEOXY-D-GLUCARATE
Ligand ExpoKGR

Enzymes

Protein Details
1. Glucarate dehydratase
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the dehydration of glucarate to 5-keto-4- deoxy-D-glucarate (5-kdGluc). Also acts on L-idarate
Gene Name:
gudD
Uniprot ID:
P0AES2
Molecular weight:
49141
Reactions
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O.
Protein Details
2. 5-keto-4-deoxy-D-glucarate aldolase
General function:
Involved in carbon-carbon lyase activity
Specific function:
Catalyzes the reversible retro-aldol cleavage of both 5- keto-4-deoxy-D-glucarate and 2-keto-3-deoxy-D-glucarate to pyruvate and tartronic semialdehyde
Gene Name:
garL
Uniprot ID:
P23522
Molecular weight:
27384
Reactions
5-dehydro-4-deoxy-D-glucarate = pyruvate + tartronate semialdehyde.
2-dehydro-3-deoxy-D-glucarate = pyruvate + tartronate semialdehyde.
Protein Details
3. D-galactarate dehydratase
General function:
Involved in hydro-lyase activity
Specific function:
D-galactarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
Gene Name:
garD
Uniprot ID:
P39829
Molecular weight:
56401
Reactions
D-galactarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O.
Protein Details
4. Glucarate dehydratase-related protein
General function:
Involved in cellular amino acid catabolic process
Specific function:
Does not seem to have an in-vivo activity on glucarate or idarate. Its real substrate is unknown
Gene Name:
gudX
Uniprot ID:
Q46915
Molecular weight:
48849