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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
Data?1676999737
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

$$$$
Download

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
PropertyValueSource
Water Solubility134 g/LALOGPS
logP-1.9ALOGPS
logP-1.8ChemAxon
logS-0.12ALOGPS
pKa (Strongest Acidic)2.91ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area115.06 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity36.32 m³·mol⁻¹ChemAxon
Polarizability15.54 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+139.02831661259
DarkChem[M-H]-133.31531661259
AllCCS[M+H]+139.70532859911
AllCCS[M-H]-132.10432859911
DeepCCS[M+H]+137.12930932474
DeepCCS[M-H]-134.73330932474
DeepCCS[M-2H]-169.64130932474
DeepCCS[M+Na]+144.32230932474
AllCCS[M+H]+139.732859911
AllCCS[M+H-H2O]+135.932859911
AllCCS[M+NH4]+143.332859911
AllCCS[M+Na]+144.332859911
AllCCS[M-H]-132.132859911
AllCCS[M+Na-2H]-133.532859911
AllCCS[M+HCOO]-135.232859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.39 minutes32390414
Predicted by Siyang on May 30, 20229.7468 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20226.85 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid270.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid723.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid312.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid41.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid178.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid63.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid272.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid246.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)668.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid592.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid44.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid854.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid190.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid210.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate633.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA312.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water357.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Keto-3-deoxy-D-gluconic acidOC[C@@H](O)[C@H](O)CC(=O)C(O)=O3134.4Standard polar33892256
2-Keto-3-deoxy-D-gluconic acidOC[C@@H](O)[C@H](O)CC(=O)C(O)=O1602.5Standard non polar33892256
2-Keto-3-deoxy-D-gluconic acidOC[C@@H](O)[C@H](O)CC(=O)C(O)=O1684.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Keto-3-deoxy-D-gluconic acid,1TMS,isomer #1C[Si](C)(C)OC[C@@H](O)[C@H](O)CC(=O)C(=O)O1678.1Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TMS,isomer #2C[Si](C)(C)O[C@H](CO)[C@H](O)CC(=O)C(=O)O1687.4Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TMS,isomer #3C[Si](C)(C)O[C@H](CC(=O)C(=O)O)[C@H](O)CO1681.8Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TMS,isomer #4C[Si](C)(C)OC(=O)C(=O)C[C@@H](O)[C@H](O)CO1663.2Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TMS,isomer #5C[Si](C)(C)OC(=C[C@@H](O)[C@H](O)CO)C(=O)O1782.2Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](O)CC(=O)C(=O)O1761.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #10C[Si](C)(C)OC(=O)C(=C[C@@H](O)[C@H](O)CO)O[Si](C)(C)C1775.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #2C[Si](C)(C)OC[C@@H](O)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C1758.3Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #3C[Si](C)(C)OC[C@@H](O)[C@H](O)CC(=O)C(=O)O[Si](C)(C)C1759.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #4C[Si](C)(C)OC[C@@H](O)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O1815.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #5C[Si](C)(C)O[C@H](CO)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C1776.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #6C[Si](C)(C)OC(=O)C(=O)C[C@@H](O)[C@@H](CO)O[Si](C)(C)C1773.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #7C[Si](C)(C)OC(=C[C@@H](O)[C@@H](CO)O[Si](C)(C)C)C(=O)O1848.6Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #8C[Si](C)(C)OC(=O)C(=O)C[C@@H](O[Si](C)(C)C)[C@H](O)CO1734.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TMS,isomer #9C[Si](C)(C)OC(=C[C@@H](O[Si](C)(C)C)[C@H](O)CO)C(=O)O1837.2Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C1813.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #10C[Si](C)(C)OC(=O)C(=C[C@@H](O[Si](C)(C)C)[C@H](O)CO)O[Si](C)(C)C1833.3Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #2C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](O)CC(=O)C(=O)O[Si](C)(C)C1836.4Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #3C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O1900.4Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #4C[Si](C)(C)OC[C@@H](O)[C@@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C1817.2Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #5C[Si](C)(C)OC[C@@H](O)[C@@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C1916.7Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #6C[Si](C)(C)OC[C@@H](O)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1824.8Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #7C[Si](C)(C)OC(=O)C(=O)C[C@@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C1827.6Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #8C[Si](C)(C)OC(=C[C@@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C)C(=O)O1904.1Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TMS,isomer #9C[Si](C)(C)OC(=O)C(=C[C@@H](O)[C@@H](CO)O[Si](C)(C)C)O[Si](C)(C)C1857.7Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C1863.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TMS,isomer #2C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C1956.8Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TMS,isomer #3C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1880.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TMS,isomer #4C[Si](C)(C)OC[C@@H](O)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C1882.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TMS,isomer #5C[Si](C)(C)OC(=O)C(=C[C@@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C)O[Si](C)(C)C1860.2Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,5TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C1894.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,5TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C1886.2Standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,5TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C1835.2Standard polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@H](O)CC(=O)C(=O)O1945.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H](CO)[C@H](O)CC(=O)C(=O)O1954.6Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H](CC(=O)C(=O)O)[C@H](O)CO1935.3Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)C(=O)C[C@@H](O)[C@H](O)CO1905.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,1TBDMS,isomer #5CC(C)(C)[Si](C)(C)OC(=C[C@@H](O)[C@H](O)CO)C(=O)O2002.6Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)CC(=O)C(=O)O2243.4Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #10CC(C)(C)[Si](C)(C)OC(=O)C(=C[C@@H](O)[C@H](O)CO)O[Si](C)(C)C(C)(C)C2215.2Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C(C)(C)C2228.1Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@H](O)CC(=O)C(=O)O[Si](C)(C)C(C)(C)C2196.7Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@H](O)C=C(O[Si](C)(C)C(C)(C)C)C(=O)O2250.9Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)O[C@H](CO)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C(C)(C)C2240.2Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)OC(=O)C(=O)C[C@@H](O)[C@@H](CO)O[Si](C)(C)C(C)(C)C2219.9Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #7CC(C)(C)[Si](C)(C)OC(=C[C@@H](O)[C@@H](CO)O[Si](C)(C)C(C)(C)C)C(=O)O2297.3Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #8CC(C)(C)[Si](C)(C)OC(=O)C(=O)C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)CO2178.7Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,2TBDMS,isomer #9CC(C)(C)[Si](C)(C)OC(=C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)CO)C(=O)O2278.9Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](CC(=O)C(=O)O)O[Si](C)(C)C(C)(C)C2480.6Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #10CC(C)(C)[Si](C)(C)OC(=O)C(=C[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)CO)O[Si](C)(C)C(C)(C)C2490.1Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)CC(=O)C(=O)O[Si](C)(C)C(C)(C)C2495.8Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)C=C(O[Si](C)(C)C(C)(C)C)C(=O)O2542.8Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](CC(=O)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2477.2Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #5CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O)O[Si](C)(C)C(C)(C)C2553.1Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #6CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@H](O)C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2459.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #7CC(C)(C)[Si](C)(C)OC(=O)C(=O)C[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[Si](C)(C)C(C)(C)C2496.6Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #8CC(C)(C)[Si](C)(C)OC(=C[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[Si](C)(C)C(C)(C)C)C(=O)O2560.6Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,3TBDMS,isomer #9CC(C)(C)[Si](C)(C)OC(=O)C(=C[C@@H](O)[C@@H](CO)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2507.1Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](CC(=O)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2703.9Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O)O[Si](C)(C)C(C)(C)C2832.8Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2726.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2747.0Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,4TBDMS,isomer #5CC(C)(C)[Si](C)(C)OC(=O)C(=C[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2722.1Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2934.5Semi standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2661.4Standard non polar33892256
2-Keto-3-deoxy-D-gluconic acid,5TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](C=C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2430.3Standard polar33892256
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