Showing metabocard for (4S)-4-hydroxy-2-oxoglutarate (MMDBc0054962)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-17 19:38:40 UTC
Update Date2025-10-07 16:08:49 UTC
Metabolite IDMMDBc0054962
Metabolite Identification
Common Name(4S)-4-hydroxy-2-oxoglutarate
Description(4S)-4-hydroxy-2-oxoglutarate is a chiral metabolite belonging to the class of organic compounds known as alpha-keto acids. Its chemical structure features a hydroxyl group at the 4-position of the 2-oxoglutarate backbone, contributing to its stereochemistry. This compound is synthesized through the action of a pyruvate-dependent aldolase, specifically the enzyme 2-oxo-3-deoxy-6-phosphogluconate aldolase (EDA), which reacts with glyoxylic acid to produce the (S)-enantiomer of (4S)-4-hydroxy-2-oxoglutarate [(S)-HOG] by introducing a chiral center (PMID:30062480 ). In biochemical pathways, (4S)-4-hydroxy-2-oxoglutarate plays a role in various metabolic processes, including amino acid metabolism and the tricarboxylic acid cycle, where it may influence the synthesis and degradation of key metabolites. Its involvement in these pathways highlights its importance in cellular metabolism and energy production.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f9ab3707830>


  Mrv1652306172221382D          

 12 11  0  0  1  0            999 V2000
    3.9039    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  1  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
    2.4750    1.4289    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
    3.1895    2.6664    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
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  5  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
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  2  6  1  6  0  0  0
  7  3  2  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  5  2  0  0  0  0
  2 12  1  6  0  0  0
M  CHG  2   9  -1  10  -1
M  END
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3D MOL for #<Metabolite:0x00007f9ab3707830>

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3D SDF for #<Metabolite:0x00007f9ab3707830>

  Mrv1652306172221382D          

 12 11  0  0  1  0            999 V2000
    3.9039    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  1  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
    2.4750    1.4289    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
    3.1895    2.6664    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
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  5  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
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  2  6  1  6  0  0  0
  7  3  2  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  5  2  0  0  0  0
  2 12  1  6  0  0  0
M  CHG  2   9  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0054962

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O6/c6-2(4(8)9)1-3(7)5(10)11/h2,6H,1H2,(H,8,9)(H,10,11)/p-2/t2-/m0/s1

> <INCHI_KEY>
WXSKVKPSMAHCSG-REOHCLBHSA-L

> <FORMULA>
C5H4O6

> <MOLECULAR_WEIGHT>
160.082

> <EXACT_MASS>
160.001885009

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.059595857861538

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-hydroxy-4-oxopentanedioate

> <JCHEM_LOGP>
-0.8244217603333331

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.331193900932066

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4491059189467634

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8864249286801433

> <JCHEM_POLAR_SURFACE_AREA>
117.56

> <JCHEM_REFRACTIVITY>
51.8954

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-hydroxy-4-oxopentanedioate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007f9ab3707830>
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PDB for #<Metabolite:0x00007f9ab3707830>
HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4    6   12                                             
CONECT    3    1    5    7                                                  
CONECT    4    2    8    9                                                  
CONECT    5    3   10   11                                                  
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for #<Metabolite:0x00007f9ab3707830>
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SMILES for #<Metabolite:0x00007f9ab3707830>
[H][C@](O)(CC(=O)C([O-])=O)C([O-])=O
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INCHI for #<Metabolite:0x00007f9ab3707830>
InChI=1S/C5H6O6/c6-2(4(8)9)1-3(7)5(10)11/h2,6H,1H2,(H,8,9)(H,10,11)/p-2/t2-/m0/s1
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Synonyms
ValueSource
(S)-2-Hydroxy-4-oxopentanedioateChEBI
(S)-2-Hydroxy-4-oxopentanedioic acidGenerator
(4S)-4-Hydroxy-2-oxoglutaric acidGenerator
Molecular FormulaC5H4O6
Average Mass160.082
Monoisotopic Mass160.001885009
IUPAC Name(2S)-2-hydroxy-4-oxopentanedioate
Traditional Name(2S)-2-hydroxy-4-oxopentanedioate
CAS Registry NumberNot Available
SMILES
[H][C@](O)(CC(=O)C([O-])=O)C([O-])=O
InChI Identifier
InChI=1S/C5H6O6/c6-2(4(8)9)1-3(7)5(10)11/h2,6H,1H2,(H,8,9)(H,10,11)/p-2/t2-/m0/s1
InChI KeyWXSKVKPSMAHCSG-REOHCLBHSA-L