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Showing metabocard for 2,3-dioxo-L-gulonate (HMDB0304040)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:39:40 UTC
Update Date2021-09-24 06:39:40 UTC
HMDB IDHMDB0304040
Secondary Accession NumbersNone
Metabolite Identification
Common Name2,3-dioxo-L-gulonate
Description2,3-dioxo-l-gulonate belongs to sugar acids and derivatives class of compounds. Those are compounds containing a saccharide unit which bears a carboxylic acid group. 2,3-dioxo-l-gulonate is soluble (in water) and a moderately acidic compound (based on its pKa). 2,3-dioxo-l-gulonate can be found in a number of food items such as gram bean, oriental wheat, agave, and horseradish, which makes 2,3-dioxo-l-gulonate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304040 (2,3-dioxo-L-gulonate)

  Mrv1533005141512312D          

 13 12  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  5  9  2  0  0  0  0
  4 10  2  0  0  0  0
  3 11  1  0  0  0  0
  2 12  1  0  0  0  0
  1 13  1  0  0  0  0
M  CHG  1   7  -1
M  END
Download

3D MOL for HMDB0304040 (2,3-dioxo-L-gulonate)

HMDB0304040
     RDKit          3D
2,3-dioxo-L-gulonate
 20 19  0  0  0  0  0  0  0  0999 V2000
    4.1123    0.2734   -0.0486 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2858    1.1406   -0.4319 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7899    2.2679   -1.0555 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.8554    1.0001   -0.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1049    1.9168   -0.6605 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2580   -0.1529    0.3987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0903   -1.0340    0.8213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1641   -0.4068    0.6125 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2890   -1.5525    1.4348 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9711   -0.6116   -0.6553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8702    0.5010   -1.4634 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4391   -0.6971   -0.2161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7333    0.4801    0.4758 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5756    0.4288    1.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3428   -1.3740    2.1964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6590   -1.5125   -1.1867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1685    0.3786   -2.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5891   -1.5634    0.4676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0884   -0.7527   -1.1111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2920    1.2702    0.1063 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
  8 14  1  0
  9 15  1  0
 10 16  1  0
 11 17  1  0
 12 18  1  0
 12 19  1  0
 13 20  1  0
M  CHG  1   3  -1
M  END
Download

3D SDF for HMDB0304040 (2,3-dioxo-L-gulonate)

  Mrv1533005141512312D          

 13 12  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  5  9  2  0  0  0  0
  4 10  2  0  0  0  0
  3 11  1  0  0  0  0
  2 12  1  0  0  0  0
  1 13  1  0  0  0  0
M  CHG  1   7  -1
M  END
> <DATABASE_ID>
HMDB0304040

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(O)C(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)/p-1

> <INCHI_KEY>
GJQWCDSAOUMKSE-UHFFFAOYSA-M

> <FORMULA>
C6H7O7

> <MOLECULAR_WEIGHT>
191.116

> <EXACT_MASS>
191.019726145

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
15.150539287497795

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5,6-trihydroxy-2,3-dioxohexanoate

> <ALOGPS_LOGP>
-1.28

> <JCHEM_LOGP>
-1.5706350913333333

> <ALOGPS_LOGS>
-0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.608625314428354

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.3785633515230975

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9800693774085065

> <JCHEM_POLAR_SURFACE_AREA>
134.96

> <JCHEM_REFRACTIVITY>
47.8751

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.40e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5,6-trihydroxy-2,3-dioxohexanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304040 (2,3-dioxo-L-gulonate)

HMDB0304040
     RDKit          3D
2,3-dioxo-L-gulonate
 20 19  0  0  0  0  0  0  0  0999 V2000
    4.1123    0.2734   -0.0486 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2858    1.1406   -0.4319 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7899    2.2679   -1.0555 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.8554    1.0001   -0.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1049    1.9168   -0.6605 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2580   -0.1529    0.3987 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0903   -1.0340    0.8213 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1641   -0.4068    0.6125 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2890   -1.5525    1.4348 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9711   -0.6116   -0.6553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8702    0.5010   -1.4634 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4391   -0.6971   -0.2161 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7333    0.4801    0.4758 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5756    0.4288    1.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3428   -1.3740    2.1964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6590   -1.5125   -1.1867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1685    0.3786   -2.3738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5891   -1.5634    0.4676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0884   -0.7527   -1.1111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2920    1.2702    0.1063 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
  8 14  1  0
  9 15  1  0
 10 16  1  0
 11 17  1  0
 12 18  1  0
 12 19  1  0
 13 20  1  0
M  CHG  1   3  -1
M  END
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PDB for HMDB0304040 (2,3-dioxo-L-gulonate)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O-1
HETATM    8  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O+0
CONECT    1    2   13                                                       
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    5                                                            
CONECT   10    4                                                            
CONECT   11    3                                                            
CONECT   12    2                                                            
CONECT   13    1                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for HMDB0304040 (2,3-dioxo-L-gulonate)

COMPND    HMDB0304040
HETATM    1  O1  UNL     1       4.112   0.273  -0.049  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.286   1.141  -0.432  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.790   2.268  -1.055  1.00  0.00           O1-
HETATM    4  C2  UNL     1       1.855   1.000  -0.246  1.00  0.00           C  
HETATM    5  O3  UNL     1       1.105   1.917  -0.660  1.00  0.00           O  
HETATM    6  C3  UNL     1       1.258  -0.153   0.399  1.00  0.00           C  
HETATM    7  O4  UNL     1       2.090  -1.034   0.821  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.164  -0.407   0.613  1.00  0.00           C  
HETATM    9  O5  UNL     1      -0.289  -1.552   1.435  1.00  0.00           O  
HETATM   10  C5  UNL     1      -0.971  -0.612  -0.655  1.00  0.00           C  
HETATM   11  O6  UNL     1      -0.870   0.501  -1.463  1.00  0.00           O  
HETATM   12  C6  UNL     1      -2.439  -0.697  -0.216  1.00  0.00           C  
HETATM   13  O7  UNL     1      -2.733   0.480   0.476  1.00  0.00           O  
HETATM   14  H1  UNL     1      -0.576   0.429   1.208  1.00  0.00           H  
HETATM   15  H2  UNL     1       0.343  -1.374   2.196  1.00  0.00           H  
HETATM   16  H3  UNL     1      -0.659  -1.512  -1.187  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.169   0.379  -2.374  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.589  -1.563   0.468  1.00  0.00           H  
HETATM   19  H6  UNL     1      -3.088  -0.753  -1.111  1.00  0.00           H  
HETATM   20  H7  UNL     1      -2.292   1.270   0.106  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5    6
CONECT    6    7    7    8
CONECT    8    9   10   14
CONECT    9   15
CONECT   10   11   12   16
CONECT   11   17
CONECT   12   13   18   19
CONECT   13   20
END
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SMILES for HMDB0304040 (2,3-dioxo-L-gulonate)

OCC(O)C(O)C(=O)C(=O)C([O-])=O
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INCHI for HMDB0304040 (2,3-dioxo-L-gulonate)

InChI=1S/C6H8O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,7-9H,1H2,(H,12,13)/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
4,5,6-Trihydroxy-2,3-dioxohexanoic acidGenerator
2,3-Dioxo-L-gulonic acidGenerator
Chemical FormulaC6H7O7
Average Molecular Weight191.116
Monoisotopic Molecular Weight191.019726145
IUPAC Name4,5,6-trihydroxy-2,3-dioxohexanoate
Traditional Name4,5,6-trihydroxy-2,3-dioxohexanoate
CAS Registry NumberNot Available
SMILES
OCC(O)C(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)/p-1
InChI KeyGJQWCDSAOUMKSE-UHFFFAOYSA-M
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
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-dioxo-L-gulonate 10V, Negative-QTOFsplash10-0fn9-7900000000-8d8219958bfbe5bfb4782019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-dioxo-L-gulonate 20V, Negative-QTOFsplash10-0pbi-9400000000-fcbb801f51380aa0e5692019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-dioxo-L-gulonate 40V, Negative-QTOFsplash10-0a4i-9000000000-3168cd32280b09116db32019-02-23Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030298
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound25202314
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available