Showing metabocard for Diketogulonic acid (MMDBc0047946)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-23 23:18:03 UTC
Update Date2024-04-30 20:33:23 UTC
Metabolite IDMMDBc0047946
Metabolite Identification
Common NameDiketogulonic acid
DescriptionDiketogulonic acid (DKG) is a metabolite of the degradation of vitamin C, the nonenzymatic hydrolysis-product of dehydroascorbate. Dehydroascorbate can be reduced back to ascorbate or hydrolyzed to DKG; the latter reaction is irreversible and DKG is devoid of antiscorbutic activity. The degradation pathway of vitamin C continues to produce l-erythrulose and oxalate as final products. DKG appears in human urine and represents approximately 20% of the vitamin C by-products (oxalate being approximately 44% and dehydroascorbate 20%). A major catabolic event in man is the cleavage of the molecule (presumably a spontaneous cleavage of DKG) between C2 and C3, with little if any decarboxylation. The oxalate formed in this way may contribute to the formation of kidney stones in susceptible individuals. However, the association between ascorbate supplementation and increased risk of kidney stone formation remains a matter of controversy. (PMID: 16698813 , 17222174 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fecd855d0d0>


  Mrv1652304202019332D          

 13 12  0  0  1  0            999 V2000
   16.4459   -3.1760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1604   -5.2385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0170   -4.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8747   -3.1760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5892   -5.2385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0181   -4.4135    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3036   -3.1760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4459   -4.0009    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1604   -4.4135    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.7315   -4.4135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8747   -4.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5892   -4.4135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3036   -4.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  6  0  0  0
  3 10  1  0  0  0  0
  4 11  2  0  0  0  0
  5 12  2  0  0  0  0
  6 13  1  0  0  0  0
  7 13  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007fecd855d0d0>

HMDB0005971
     RDKit          3D
Diketogulonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    3.4493   -1.7249    0.2818 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2503   -0.5263   -0.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2897    0.2444   -0.5258 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9135    0.0636    0.1296 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7252    1.2631   -0.1853 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8108   -0.7263    0.6471 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0412   -1.9326    0.9596 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5365   -0.1322    0.8015 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3567   -1.1420    1.3568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0413    0.2459   -0.5755 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0027   -0.8711   -1.3746 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4890    0.7324   -0.4836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5338    1.8690    0.3285 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9476   -0.2021   -1.1424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5387    0.7705    1.4295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2112   -0.7652    1.6856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4383    1.0531   -0.9994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5849   -1.5670   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8358    1.0106   -1.4858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1345   -0.0765   -0.0829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7241    2.4138    0.2559 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  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
  8 15  1  1
  9 16  1  0
 10 17  1  6
 11 18  1  0
 12 19  1  0
 12 20  1  0
 13 21  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007fecd855d0d0>


  Mrv1652304202019332D          

 13 12  0  0  1  0            999 V2000
   16.4459   -3.1760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1604   -5.2385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0170   -4.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8747   -3.1760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5892   -5.2385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0181   -4.4135    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3036   -3.1760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4459   -4.0009    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1604   -4.4135    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.7315   -4.4135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8747   -4.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5892   -4.4135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3036   -4.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  6  0  0  0
  3 10  1  0  0  0  0
  4 11  2  0  0  0  0
  5 12  2  0  0  0  0
  6 13  1  0  0  0  0
  7 13  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0047946

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,7-9H,1H2,(H,12,13)/t2-,3+/m0/s1

> <INCHI_KEY>
GJQWCDSAOUMKSE-STHAYSLISA-N

> <FORMULA>
C6H8O7

> <MOLECULAR_WEIGHT>
192.1235

> <EXACT_MASS>
192.02700261

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
15.881992851747036

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5S)-4,5,6-trihydroxy-2,3-dioxohexanoic acid

> <ALOGPS_LOGP>
-1.77

> <JCHEM_LOGP>
-1.5706350913333333

> <ALOGPS_LOGS>
-0.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.608625314428354

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.3785633515230993

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9800693774085065

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
37.038000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.99e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
diketogulonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fecd855d0d0>

HMDB0005971
     RDKit          3D
Diketogulonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    3.4493   -1.7249    0.2818 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2503   -0.5263   -0.0301 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2897    0.2444   -0.5258 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9135    0.0636    0.1296 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7252    1.2631   -0.1853 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8108   -0.7263    0.6471 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0412   -1.9326    0.9596 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5365   -0.1322    0.8015 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3567   -1.1420    1.3568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0413    0.2459   -0.5755 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0027   -0.8711   -1.3746 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4890    0.7324   -0.4836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5338    1.8690    0.3285 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9476   -0.2021   -1.1424 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5387    0.7705    1.4295 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2112   -0.7652    1.6856 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4383    1.0531   -0.9994 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5849   -1.5670   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8358    1.0106   -1.4858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1345   -0.0765   -0.0829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7241    2.4138    0.2559 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  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
  8 15  1  1
  9 16  1  0
 10 17  1  6
 11 18  1  0
 12 19  1  0
 12 20  1  0
 13 21  1  0
M  END
Download

PDB for #<Metabolite:0x00007fecd855d0d0>

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  O   UNK     0      30.699  -5.929   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      32.033  -9.779   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      28.032  -7.468   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      33.366  -5.929   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      34.700  -9.779   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      37.367  -8.239   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      36.033  -5.929   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      30.699  -7.468   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      32.033  -8.239   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      29.365  -8.239   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      33.366  -7.468   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      34.700  -8.239   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      36.033  -7.468   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4   11                                                            
CONECT    5   12                                                            
CONECT    6   13                                                            
CONECT    7   13                                                            
CONECT    8    1    9   10                                                  
CONECT    9    2    8   11                                                  
CONECT   10    3    8                                                       
CONECT   11    4    9   12                                                  
CONECT   12    5   11   13                                                  
CONECT   13    6    7   12                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for #<Metabolite:0x00007fecd855d0d0>

COMPND    HMDB0005971
HETATM    1  O1  UNL     1       3.449  -1.725   0.282  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.250  -0.526  -0.030  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.290   0.244  -0.526  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.914   0.064   0.130  1.00  0.00           C  
HETATM    5  O3  UNL     1       1.725   1.263  -0.185  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.811  -0.726   0.647  1.00  0.00           C  
HETATM    7  O4  UNL     1       1.041  -1.933   0.960  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.536  -0.132   0.802  1.00  0.00           C  
HETATM    9  O5  UNL     1      -1.357  -1.142   1.357  1.00  0.00           O  
HETATM   10  C5  UNL     1      -1.041   0.246  -0.575  1.00  0.00           C  
HETATM   11  O6  UNL     1      -1.003  -0.871  -1.375  1.00  0.00           O  
HETATM   12  C6  UNL     1      -2.489   0.732  -0.484  1.00  0.00           C  
HETATM   13  O7  UNL     1      -2.534   1.869   0.329  1.00  0.00           O  
HETATM   14  H1  UNL     1       4.948  -0.202  -1.142  1.00  0.00           H  
HETATM   15  H2  UNL     1      -0.539   0.770   1.430  1.00  0.00           H  
HETATM   16  H3  UNL     1      -2.211  -0.765   1.686  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.438   1.053  -0.999  1.00  0.00           H  
HETATM   18  H5  UNL     1      -1.585  -1.567  -0.991  1.00  0.00           H  
HETATM   19  H6  UNL     1      -2.836   1.011  -1.486  1.00  0.00           H  
HETATM   20  H7  UNL     1      -3.135  -0.076  -0.083  1.00  0.00           H  
HETATM   21  H8  UNL     1      -1.724   2.414   0.256  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5    5    6
CONECT    6    7    7    8
CONECT    8    9   10   15
CONECT    9   16
CONECT   10   11   12   17
CONECT   11   18
CONECT   12   13   19   20
CONECT   13   21
END
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SMILES for #<Metabolite:0x00007fecd855d0d0>

OC[C@H](O)[C@@H](O)C(=O)C(=O)C(O)=O
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INCHI for #<Metabolite:0x00007fecd855d0d0>

InChI=1S/C6H8O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,7-9H,1H2,(H,12,13)/t2-,3+/m0/s1
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Synonyms
ValueSource
(4R,5S)-2,3-Dioxo-4,5,6-trihydroxyhexanoic acidChEBI
(4R,5S)-4,5,6-Trihydroxy-2,3-dioxohexanoateChEBI
(4R,5S)-4,5,6-Trihydroxy-2,3-dioxohexanoic acidChEBI
2,3-Diketo-L-gulonateChEBI
2,3-Diketo-L-gulonic acidChEBI
2,3-Dioxo-2,3-dideoxy-L-gulonic acidChEBI
2,3-L-Diketogulonic acidChEBI
Diketo-L-gulonic acidChEBI
L-Threo-(2,3)-hexodiulosonsaeureChEBI
L-Threo-2,3-hexodiurosonic acidChEBI
Threo-2,3-hexodiulosonic acidChEBI
(4R,5S)-2,3-Dioxo-4,5,6-trihydroxyhexanoateGenerator
2,3-Dioxo-2,3-dideoxy-L-gulonateGenerator
2,3-L-DiketogulonateGenerator
Diketo-L-gulonateGenerator
L-Threo-2,3-hexodiurosonateGenerator
Threo-2,3-hexodiulosonateGenerator
DiketogulonateGenerator
2,3-Diketogulonic acidHMDB
2,3-Dioxo-D-gulonateHMDB
L-Threo-2,3-hexodiulosonic acidHMDB
L-Threo-hexo-2,3-diulosonic acidHMDB
Acid, 2,3-diketogulonicHMDB
2,3 Diketogulonic acidHMDB
Diketo-gulonateHMDB
2,3-DiketogulonateHMDB
Molecular FormulaC6H8O7
Average Mass192.1235
Monoisotopic Mass192.02700261
IUPAC Name(4R,5S)-4,5,6-trihydroxy-2,3-dioxohexanoic acid
Traditional Namediketogulonic acid
CAS Registry Number3409-57-2
SMILES
OC[C@H](O)[C@@H](O)C(=O)C(=O)C(O)=O
InChI Identifier
InChI=1S/C6H8O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,7-9H,1H2,(H,12,13)/t2-,3+/m0/s1
InChI KeyGJQWCDSAOUMKSE-STHAYSLISA-N