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Showing NP-Card for Diketogulonic acid (NP0136744)

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Record Information
Version2.0
Created at2022-05-12 15:22:25 UTC
Updated at2022-05-12 15:22:25 UTC
NP-MRD IDNP0136744
Secondary Accession NumbersNone
Natural Product Identification
Common NameDiketogulonic acid
DescriptionDiketogulonic acid, also known as 2,3-diketo-L-gulonate, belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. Diketogulonic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Diketogulonic acid exists in all living organisms, ranging from bacteria to humans. Dehydroascorbate can be reduced back to ascorbate or hydrolyzed to DKG; the latter reaction is irreversible and DKG is devoid of antiscorbutic activity. DKG appears in human urine and represents approximately 20% of the vitamin C by-products (oxalate being approximately 44% and dehydroascorbate 20%). However, the association between ascorbate supplementation and increased risk of kidney stone formation remains a matter of controversy. The oxalate formed in this way may contribute to the formation of kidney stones in susceptible individuals. Diketogulonic acid (DKG) is a metabolite of the degradation of vitamin C, the nonenzymatic hydrolysis-product of dehydroascorbate. 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. Diketogulonic acid was first documented in 1998 (PMID: 9506998). The degradation pathway of vitamin C continues to produce l-erythrulose and oxalate as final products (PMID: 17222174) (PMID: 16698813).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0136744 (Diketogulonic acid)


  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 NP0136744 (Diketogulonic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
    3.7733    0.2601   -0.6434 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3918   -0.0905    0.4908 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2984   -0.5738    1.4098 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9951    0.0090    0.8457 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6067   -0.3435    1.9878 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0440    0.5149   -0.1151 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3999    0.8755   -1.2649 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4106    0.6395    0.1969 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6795    0.2175    1.4747 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2293   -0.0356   -0.8646 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0569   -1.4010   -0.9056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6952    0.3326   -0.6732 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1860   -0.1956    0.5190 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1653   -0.0717    1.5897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6813    1.7339    0.1546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6996   -0.7522    1.5927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9153    0.3872   -1.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4512   -1.8552   -0.1183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7865    1.4334   -0.5894 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3080    0.0087   -1.5363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5752   -1.0930    0.3408 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 10  1  0
 10 11  1  0
 10  8  1  0
  8  9  1  0
  8  6  1  0
  6  7  2  0
  6  4  1  0
  4  5  2  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 13 21  1  0
 12 19  1  0
 12 20  1  0
 10 17  1  6
 11 18  1  0
  8 15  1  1
  9 16  1  0
  3 14  1  0
M  END
Download

3D SDF for NP0136744 (Diketogulonic acid)


  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>
NP0136744

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
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3D-SDF for NP0136744 (Diketogulonic acid)

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PDB for NP0136744 (Diketogulonic acid)
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 NP0136744 (Diketogulonic acid)
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SMILES for NP0136744 (Diketogulonic acid)
OC[C@H](O)[C@@H](O)C(=O)C(=O)C(O)=O
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INCHI for NP0136744 (Diketogulonic acid)
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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View in JSmol
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-gulonateGenerator
2,3-DiketogulonateGenerator
Chemical FormulaC6H8O7
Average Mass192.1235 Da
Monoisotopic Mass192.02700 Da
IUPAC Name(4R,5S)-4,5,6-trihydroxy-2,3-dioxohexanoic acid
Traditional Namediketogulonic acid
CAS Registry NumberNot Available
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
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentSugar acids and derivatives  
Alternative Parents
Substituents
  • Hexose monosaccharide
    • 

  • Medium-chain keto acid
    • 

  • Beta-keto acid
    • 

  • Sugar acid
    • 

  • Acyloin
    • 

  • Alpha-keto acid
    • 

  • Alpha-diketone
    • 

  • Beta-hydroxy ketone
    • 

  • Keto acid
    • 

  • Monosaccharide
    • 

  • Alpha-hydroxy ketone
    • 

  • Ketone
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Organic oxide
    • 

  • Primary alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.8ALOGPS
logP-1.6ChemAxon
logS-0.51ALOGPS
pKa (Strongest Acidic)2.38ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.04 m³·mol⁻¹ChemAxon
Polarizability15.88 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0005971  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID389343  
KEGG Compound IDC04575  
BioCyc IDCPD-334  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440390  
PDB IDNot Available
ChEBI ID15622  
Good Scents IDNot Available
References
General References
  1. Shamsi FA, Partal A, Sady C, Glomb MA, Nagaraj RH: Immunological evidence for methylglyoxal-derived modifications in vivo. Determination of antigenic epitopes. J Biol Chem. 1998 Mar 20;273(12):6928-36. doi: 10.1074/jbc.273.12.6928. [PubMed:9506998  ] 
  2. Linster CL, Van Schaftingen E: Vitamin C. Biosynthesis, recycling and degradation in mammals. FEBS J. 2007 Jan;274(1):1-22. doi: 10.1111/j.1742-4658.2006.05607.x. [PubMed:17222174  ] 
  3. Karkonen A, Fry SC: Effect of ascorbate and its oxidation products on H2O2 production in cell-suspension cultures of Picea abies and in the absence of cells. J Exp Bot. 2006;57(8):1633-44. doi: 10.1093/jxb/erj197. Epub 2006 May 12. [PubMed:16698813  ]