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Showing metabocard for 2-Keto-3-deoxy-D-gluconic acid (HMDB0001353)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:37 UTC
HMDB IDHMDB0001353
Secondary Accession Numbers
  • HMDB01353
Metabolite Identification
Common Name2-Keto-3-deoxy-D-gluconic acid
Description2-Keto-3-deoxy-D-gluconic acid, also known as 2-dehydro-3-deoxy-D-galactonate, 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. 2-Keto-3-deoxy-D-gluconic acid exists in all living organisms, ranging from bacteria to humans. 2-Keto-3-deoxy-D-gluconic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 2-keto-3-deoxy-D-gluconic acid a potential biomarker for the consumption of these foods. 2-Keto-3-deoxy-D-gluconic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on 2-Keto-3-deoxy-D-gluconic acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001353 (2-Keto-3-deoxy-D-gluconic acid)

  Mrv0541 02231219052D          

 12 11  0  0  1  0            999 V2000
    2.7165   -4.7233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310   -4.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310   -3.4858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1454   -4.7233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1454   -5.5483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8599   -4.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5744   -4.7233    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5744   -5.5483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2888   -4.3108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2888   -3.4858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0033   -4.7233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7177   -4.3108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  7  8  1  6  0  0  0
  9  7  1  0  0  0  0
  9 10  1  6  0  0  0
 11  9  1  0  0  0  0
 12 11  1  0  0  0  0
M  END
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3D MOL for HMDB0001353 (2-Keto-3-deoxy-D-gluconic acid)

HMDB0001353
     RDKit          3D
2-Keto-3-deoxy-D-gluconic acid
 22 21  0  0  0  0  0  0  0  0999 V2000
    3.0193   -1.3346   -1.1727 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1495   -0.3287   -0.4299 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3854    0.2780   -0.2792 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0202    0.2238    0.2866 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1333    1.2264    1.0312 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -0.4130    0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3480    0.3276    0.9752 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4367    1.6540    0.5619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7108   -0.3046    0.8414 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6300   -1.6354    1.2534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2265   -0.2126   -0.5647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2852    1.1437   -0.9226 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6029    0.7616    0.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7265   -1.4680    0.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3788   -0.2983   -0.9299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0320    0.3267    2.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0020    1.7994   -0.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4253    0.2249    1.4931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2655   -2.1838    0.7033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5778   -0.7581   -1.2677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2464   -0.6488   -0.5705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9185    1.6199   -0.3389 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
  3 13  1  0
  6 14  1  0
  6 15  1  0
  7 16  1  1
  8 17  1  0
  9 18  1  1
 10 19  1  0
 11 20  1  0
 11 21  1  0
 12 22  1  0
M  END
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3D SDF for HMDB0001353 (2-Keto-3-deoxy-D-gluconic acid)

  Mrv0541 02231219052D          

 12 11  0  0  1  0            999 V2000
    2.7165   -4.7233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310   -4.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4310   -3.4858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1454   -4.7233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1454   -5.5483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8599   -4.3108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5744   -4.7233    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5744   -5.5483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2888   -4.3108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2888   -3.4858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0033   -4.7233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7177   -4.3108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  7  8  1  6  0  0  0
  9  7  1  0  0  0  0
  9 10  1  6  0  0  0
 11  9  1  0  0  0  0
 12 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001353

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@@H](O)[C@H](O)CC(=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5-/m1/s1

> <INCHI_KEY>
WPAMZTWLKIDIOP-NQXXGFSBSA-N

> <FORMULA>
C6H10O6

> <MOLECULAR_WEIGHT>
178.14

> <EXACT_MASS>
178.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
15.535652108876848

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid

> <ALOGPS_LOGP>
-1.87

> <JCHEM_LOGP>
-1.7750312403333335

> <ALOGPS_LOGS>
-0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.243645462336318

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9051234753891952

> <JCHEM_PKA_STRONGEST_BASIC>
-2.972361954381558

> <JCHEM_POLAR_SURFACE_AREA>
115.06

> <JCHEM_REFRACTIVITY>
36.3163

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.34e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001353 (2-Keto-3-deoxy-D-gluconic acid)

HMDB0001353
     RDKit          3D
2-Keto-3-deoxy-D-gluconic acid
 22 21  0  0  0  0  0  0  0  0999 V2000
    3.0193   -1.3346   -1.1727 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1495   -0.3287   -0.4299 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3854    0.2780   -0.2792 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0202    0.2238    0.2866 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1333    1.2264    1.0312 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -0.4130    0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3480    0.3276    0.9752 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4367    1.6540    0.5619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7108   -0.3046    0.8414 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6300   -1.6354    1.2534 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2265   -0.2126   -0.5647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2852    1.1437   -0.9226 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6029    0.7616    0.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7265   -1.4680    0.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3788   -0.2983   -0.9299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0320    0.3267    2.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0020    1.7994   -0.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4253    0.2249    1.4931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2655   -2.1838    0.7033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5778   -0.7581   -1.2677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2464   -0.6488   -0.5705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9185    1.6199   -0.3389 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  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
  3 13  1  0
  6 14  1  0
  6 15  1  0
  7 16  1  1
  8 17  1  0
  9 18  1  1
 10 19  1  0
 11 20  1  0
 11 21  1  0
 12 22  1  0
M  END
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PDB for HMDB0001353 (2-Keto-3-deoxy-D-gluconic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       5.071  -8.817   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.405  -8.047   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       6.405  -6.507   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       7.738  -8.817   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       7.738 -10.357   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       9.072  -8.047   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.406  -8.817   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      10.406 -10.357   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      11.739  -8.047   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.739  -6.507   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.073  -8.817   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      14.406  -8.047   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for HMDB0001353 (2-Keto-3-deoxy-D-gluconic acid)

COMPND    HMDB0001353
HETATM    1  O1  UNL     1       3.019  -1.335  -1.173  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.149  -0.329  -0.430  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.385   0.278  -0.279  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.020   0.224   0.287  1.00  0.00           C  
HETATM    5  O3  UNL     1       2.133   1.226   1.031  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.685  -0.413   0.138  1.00  0.00           C  
HETATM    7  C4  UNL     1      -0.348   0.328   0.975  1.00  0.00           C  
HETATM    8  O4  UNL     1      -0.437   1.654   0.562  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.711  -0.305   0.841  1.00  0.00           C  
HETATM   10  O5  UNL     1      -1.630  -1.635   1.253  1.00  0.00           O  
HETATM   11  C6  UNL     1      -2.226  -0.213  -0.565  1.00  0.00           C  
HETATM   12  O6  UNL     1      -2.285   1.144  -0.923  1.00  0.00           O  
HETATM   13  H1  UNL     1       4.603   0.762   0.577  1.00  0.00           H  
HETATM   14  H2  UNL     1       0.727  -1.468   0.454  1.00  0.00           H  
HETATM   15  H3  UNL     1       0.379  -0.298  -0.930  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.032   0.327   2.035  1.00  0.00           H  
HETATM   17  H5  UNL     1       0.002   1.799  -0.304  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.425   0.225   1.493  1.00  0.00           H  
HETATM   19  H7  UNL     1      -2.265  -2.184   0.703  1.00  0.00           H  
HETATM   20  H8  UNL     1      -1.578  -0.758  -1.268  1.00  0.00           H  
HETATM   21  H9  UNL     1      -3.246  -0.649  -0.571  1.00  0.00           H  
HETATM   22  H10 UNL     1      -2.919   1.620  -0.339  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5    5    6
CONECT    6    7   14   15
CONECT    7    8    9   16
CONECT    8   17
CONECT    9   10   11   18
CONECT   10   19
CONECT   11   12   20   21
CONECT   12   22
END
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SMILES for HMDB0001353 (2-Keto-3-deoxy-D-gluconic acid)

OC[C@@H](O)[C@H](O)CC(=O)C(O)=O
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INCHI for HMDB0001353 (2-Keto-3-deoxy-D-gluconic acid)

InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Dehydro-3-deoxy-D-galactonateChEBI
2-Dehydro-3-deoxy-D-galactonic acidGenerator
2-Keto-3-deoxy-D-gluconateGenerator
2-oxo-3-Deoxygalactonic acidMeSH, HMDB
3-Deoxy-D-threo-hexulosonic acidMeSH, HMDB
Chemical FormulaC6H10O6
Average Molecular Weight178.14
Monoisotopic Molecular Weight178.047738052
IUPAC Name(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid
Traditional Name(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid
CAS Registry Number17510-99-5
SMILES
OC[C@@H](O)[C@H](O)CC(=O)C(O)=O
InChI Identifier
InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5-/m1/s1
InChI KeyWPAMZTWLKIDIOP-NQXXGFSBSA-N
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
  • Alpha-keto acid
  • Beta-hydroxy ketone
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • Polyol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Primary alcohol
  • Organooxygen compound
  • Organic oxygen compound
  • Carbonyl group
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
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 Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022572
KNApSAcK IDNot Available
Chemspider ID168361
KEGG Compound IDC01216
BioCyc ID2-DEHYDRO-3-DEOXY-D-GLUCONATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6184
PubChem Compound194024
PDB IDNot Available
ChEBI ID17028
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferencePlantier-Royon, Richard; Anker, Daniel; Robert-Baudouy, , Janine. New synthesis of 3-deoxy-D-erythro-2-hexulosonic acid (KDG) from D-glucose. Journal of Carbohydrate Chemistry (1991), 10(2), 239-49.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available