Showing metabocard for 2-Keto-3-deoxy-D-gluconic acid (MMDBc0000388)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:36:40 UTC
Update Date2022-08-31 06:03:00 UTC
Metabolite IDMMDBc0000388
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645ca09ef00>


  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
Download

3D MOL for #<Metabolite:0x00005645ca09ef00>

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
Download

3D SDF for #<Metabolite:0x00005645ca09ef00>


  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>
MMDBc0000388

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00005645ca09ef00>

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 #<Metabolite:0x00005645ca09ef00>

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 #<Metabolite:0x00005645ca09ef00>

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 #<Metabolite:0x00005645ca09ef00>

OC[C@@H](O)[C@H](O)CC(=O)C(O)=O
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INCHI for #<Metabolite:0x00005645ca09ef00>

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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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
Molecular FormulaC6H10O6
Average Mass178.14
Monoisotopic Mass178.047738052
IUPAC Name(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid
Traditional Name(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid
CAS Registry NumberNot Available
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