Showing metabocard for 5-Keto-D-gluconate (MMDBc0029913)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:46:37 UTC
Update Date2022-08-31 17:37:35 UTC
Metabolite IDMMDBc0029913
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.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923c039758>


  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 #<Metabolite:0x00007f923c039758>

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 #<Metabolite:0x00007f923c039758>


  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>
MMDBc0029913

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f923c039758>

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 #<Metabolite:0x00007f923c039758>

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 #<Metabolite:0x00007f923c039758>

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 #<Metabolite:0x00007f923c039758>

OCC(=O)C(O)C(O)C(O)C(O)=O
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INCHI for #<Metabolite:0x00007f923c039758>

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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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
Molecular FormulaC6H10O7
Average Mass194.1394
Monoisotopic Mass194.042652674
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