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Showing metabocard for 5-Keto-D-gluconate (HMDB0011731)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-03-03 10:13:10 UTC
Update Date2022-03-07 02:51:13 UTC
HMDB IDHMDB0011731
Secondary Accession Numbers
  • HMDB11731
Metabolite Identification
Common Name5-Keto-D-gluconate
Description5-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. 5-Keto-D-gluconate has also been found to be a metabolite of Gluconobacter (https://www.sciencedirect.com/science/article/pii/S138111779800112X).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011731 (5-Keto-D-gluconate)

  Mrv0541 02241201522D          

 13 12  0  0  0  0            999 V2000
   15.5803  -11.4006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9928  -12.1151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5803  -12.8295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7553  -12.8295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3428  -13.5440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7553  -14.2585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7553  -11.4006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8178  -12.1151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9928  -13.5440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3428  -12.1151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5178  -13.5440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3428  -14.9730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5803  -14.2585    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1  2  1  0  0  0  0
  2  8  2  0  0  0  0
  2  3  1  0  0  0  0
  3  9  1  0  0  0  0
  3  4  1  0  0  0  0
  4 10  1  0  0  0  0
  4  5  1  0  0  0  0
  5 11  1  0  0  0  0
  5  6  1  0  0  0  0
  6 12  1  0  0  0  0
  6 13  2  0  0  0  0
M  END
Download

3D MOL for HMDB0011731 (5-Keto-D-gluconate)

HMDB0011731
     RDKit          3D
5-Keto-D-gluconate
 23 22  0  0  0  0  0  0  0  0999 V2000
   -3.3713   -1.2590   -0.0215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7467   -0.2137    0.2523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4092    0.9871    0.2931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737   -0.3191    0.5293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9129   -1.6374    0.4121 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6046    0.6133   -0.4420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274    1.8869   -0.1640 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8559    0.9192   -0.1526 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0943    2.0072   -1.0896 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8136   -0.1136   -0.5569 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2149   -0.1044   -1.7208 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3457   -1.1640    0.3266 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2653   -1.9935   -0.3680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3779    1.0948    0.5632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1015    0.0379    1.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8857   -2.1056    1.2766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7347    0.3347   -1.4906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1006    1.9684    0.8294 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9931    1.3345    0.8443 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7842    1.7138   -1.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8808   -0.7006    1.2125 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6217   -1.8455    0.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8768   -1.4415   -0.9232 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 12 21  1  0
 12 22  1  0
 13 23  1  0
M  END
Download

3D SDF for HMDB0011731 (5-Keto-D-gluconate)

  Mrv0541 02241201522D          

 13 12  0  0  0  0            999 V2000
   15.5803  -11.4006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9928  -12.1151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5803  -12.8295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7553  -12.8295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3428  -13.5440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7553  -14.2585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7553  -11.4006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8178  -12.1151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9928  -13.5440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3428  -12.1151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5178  -13.5440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3428  -14.9730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5803  -14.2585    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1  2  1  0  0  0  0
  2  8  2  0  0  0  0
  2  3  1  0  0  0  0
  3  9  1  0  0  0  0
  3  4  1  0  0  0  0
  4 10  1  0  0  0  0
  4  5  1  0  0  0  0
  5 11  1  0  0  0  0
  5  6  1  0  0  0  0
  6 12  1  0  0  0  0
  6 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011731

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(=O)C(O)C(O)C(O)C(O)=O

> <INCHI_IDENTIFIER>
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)

> <INCHI_KEY>
IZSRJDGCGRAUAR-UHFFFAOYSA-N

> <FORMULA>
C6H10O7

> <MOLECULAR_WEIGHT>
194.1394

> <EXACT_MASS>
194.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
16.141986513797647

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4,6-tetrahydroxy-5-oxohexanoic acid

> <ALOGPS_LOGP>
-2.51

> <JCHEM_LOGP>
-2.946757354

> <ALOGPS_LOGS>
-0.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.187174008997602

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.237703039512069

> <JCHEM_PKA_STRONGEST_BASIC>
-3.327640252947691

> <JCHEM_POLAR_SURFACE_AREA>
135.29000000000002

> <JCHEM_REFRACTIVITY>
37.4292

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.12e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-xylo-5-hexulosonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0011731 (5-Keto-D-gluconate)

HMDB0011731
     RDKit          3D
5-Keto-D-gluconate
 23 22  0  0  0  0  0  0  0  0999 V2000
   -3.3713   -1.2590   -0.0215 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7467   -0.2137    0.2523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4092    0.9871    0.2931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737   -0.3191    0.5293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9129   -1.6374    0.4121 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6046    0.6133   -0.4420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274    1.8869   -0.1640 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8559    0.9192   -0.1526 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0943    2.0072   -1.0896 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8136   -0.1136   -0.5569 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2149   -0.1044   -1.7208 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3457   -1.1640    0.3266 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2653   -1.9935   -0.3680 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3779    1.0948    0.5632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1015    0.0379    1.5937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8857   -2.1056    1.2766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7347    0.3347   -1.4906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1006    1.9684    0.8294 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9931    1.3345    0.8443 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7842    1.7138   -1.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8808   -0.7006    1.2125 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6217   -1.8455    0.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8768   -1.4415   -0.9232 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 12 21  1  0
 12 22  1  0
 13 23  1  0
M  END
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PDB for HMDB0011731 (5-Keto-D-gluconate)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      29.083 -21.281   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      29.853 -22.615   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      29.083 -23.948   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.543 -23.948   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      26.773 -25.282   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.543 -26.616   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      27.543 -21.281   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      31.393 -22.615   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      29.853 -25.282   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      26.773 -22.615   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      25.233 -25.282   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      26.773 -27.950   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      29.083 -26.616   0.000  0.00  0.00           O+0
CONECT    1    7    2                                                       
CONECT    2    1    8    3                                                  
CONECT    3    2    9    4                                                  
CONECT    4    3   10    5                                                  
CONECT    5    4   11    6                                                  
CONECT    6    5   12   13                                                  
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0011731 (5-Keto-D-gluconate)

COMPND    HMDB0011731
HETATM    1  O1  UNL     1      -3.371  -1.259  -0.022  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.747  -0.214   0.252  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.409   0.987   0.293  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.274  -0.319   0.529  1.00  0.00           C  
HETATM    5  O3  UNL     1      -0.913  -1.637   0.412  1.00  0.00           O  
HETATM    6  C3  UNL     1      -0.605   0.613  -0.442  1.00  0.00           C  
HETATM    7  O4  UNL     1      -1.227   1.887  -0.164  1.00  0.00           O  
HETATM    8  C4  UNL     1       0.856   0.919  -0.153  1.00  0.00           C  
HETATM    9  O5  UNL     1       1.094   2.007  -1.090  1.00  0.00           O  
HETATM   10  C5  UNL     1       1.814  -0.114  -0.557  1.00  0.00           C  
HETATM   11  O6  UNL     1       2.215  -0.104  -1.721  1.00  0.00           O  
HETATM   12  C6  UNL     1       2.346  -1.164   0.327  1.00  0.00           C  
HETATM   13  O7  UNL     1       3.265  -1.994  -0.368  1.00  0.00           O  
HETATM   14  H1  UNL     1      -4.378   1.095   0.563  1.00  0.00           H  
HETATM   15  H2  UNL     1      -1.102   0.038   1.594  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.886  -2.106   1.277  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.735   0.335  -1.491  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.101   1.968   0.829  1.00  0.00           H  
HETATM   19  H6  UNL     1       0.993   1.335   0.844  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.784   1.714  -1.983  1.00  0.00           H  
HETATM   21  H8  UNL     1       2.881  -0.701   1.213  1.00  0.00           H  
HETATM   22  H9  UNL     1       1.622  -1.845   0.779  1.00  0.00           H  
HETATM   23  H10 UNL     1       3.877  -1.442  -0.923  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5    6   15
CONECT    5   16
CONECT    6    7    8   17
CONECT    7   18
CONECT    8    9   10   19
CONECT    9   20
CONECT   10   11   11   12
CONECT   12   13   21   22
CONECT   13   23
END
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SMILES for HMDB0011731 (5-Keto-D-gluconate)

OCC(=O)C(O)C(O)C(O)C(O)=O
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INCHI for HMDB0011731 (5-Keto-D-gluconate)

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)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-DehydrogluconateKegg
5-Dehydrogluconic acidGenerator
5-Keto-D-gluconic acidGenerator
D-Lyxo-5-hexulosonic acidMeSH
5-dehydro-D-GluconateHMDB
5-K-GluconateHMDB
5-KetogluconateHMDB
5K-GluconateHMDB
D-TagaturonateHMDB
D-Tagaturonic acidHMDB
Hex-5-ulosonic acidHMDB
TagaturonateHMDB
Chemical FormulaC6H10O7
Average Molecular Weight194.1394
Monoisotopic Molecular Weight194.042652674
IUPAC Name2,3,4,6-tetrahydroxy-5-oxohexanoic acid
Traditional NameD-xylo-5-hexulosonic acid
CAS Registry Number3470-36-8
SMILES
OCC(=O)C(O)C(O)C(O)C(O)=O
InChI Identifier
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)
InChI KeyIZSRJDGCGRAUAR-UHFFFAOYSA-N
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassMedium-chain hydroxy acids and derivatives
Direct ParentMedium-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Beta-hydroxy acid
  • Hydroxy fatty acid
  • Acyloin
  • Alpha-hydroxy acid
  • Beta-hydroxy ketone
  • Monosaccharide
  • Fatty acyl
  • Fatty acid
  • Alpha-hydroxy ketone
  • Ketone
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Polyol
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Organooxygen compound
  • Primary alcohol
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028411
KNApSAcK IDNot Available
Chemspider ID152
KEGG Compound IDC01062
BioCyc IDCPD-645
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound157
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDTAGUR
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available