Showing metabocard for Oxoglutaric acid (MMDBc0000067)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:29:11 UTC
Update Date2024-10-09 16:31:37 UTC
Metabolite IDMMDBc0000067
Metabolite Identification
Common NameOxoglutaric acid
DescriptionOxoglutaric acid, also known as alpha-ketoglutarate, alpha-ketoglutaric acid, AKG, or 2-oxoglutaric acid, is classified as a gamma-keto acid or a gamma-keto acid derivative. gamma-Keto acids are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom. alpha-Ketoglutarate is considered to be soluble (in water) and acidic. alpha-Ketoglutarate is a key molecule in the TCA cycle, playing a fundamental role in determining the overall rate of this important metabolic process (PMID: 26759695 ). In the TCA cycle, AKG is decarboxylated to succinyl-CoA and carbon dioxide by AKG dehydrogenase, which functions as a key control point of the TCA cycle. Additionally, AKG can be generated from isocitrate by oxidative decarboxylation catalyzed by the enzyme known as isocitrate dehydrogenase (IDH). In addition to these routes of production, AKG can be produced from glutamate by oxidative deamination via glutamate dehydrogenase, and as a product of pyridoxal phosphate-dependent transamination reactions (mediated by branched-chain amino acid transaminases) in which glutamate is a common amino donor. AKG is a nitrogen scavenger and a source of glutamate and glutamine that stimulates protein synthesis and inhibits protein degradation in muscles. In particular, AKG can decrease protein catabolism and increase protein synthesis to enhance bone tissue formation in skeletal muscles (PMID: 26759695 ). Interestingly, enteric feeding of AKG supplements can significantly increase circulating plasma levels of hormones such as insulin, growth hormone, and insulin-like growth factor-1 (PMID: 26759695 ). It has recently been shown that AKG can extend the lifespan of adult C. elegans by inhibiting ATP synthase and TOR (PMID: 24828042 ). In combination with molecular oxygen, alpha-ketoglutarate is required for the hydroxylation of proline to hydroxyproline in the production of type I collagen. A recent study has shown that alpha-ketoglutarate promotes TH1 differentiation along with the depletion of glutamine thereby favouring Treg (regulatory T-cell) differentiation (PMID: 26420908 ). alpha-Ketoglutarate has been found to be associated with fumarase deficiency, 2-ketoglutarate dehydrogenase complex deficiency, and D-2-hydroxyglutaric aciduria, which are all inborn errors of metabolism (PMID: 8338207 ). Oxoglutaric acid has been found to be a metabolite produced by Corynebacterium and yeast (PMID: 27872963 ) (YMDB).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f46c5579488>

HMDB01645_MOL.mol
  Mrv1652309032023562D          

 10  9  0  0  0  0            999 V2000
    1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.0313    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
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  2 10  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f46c5579488>

HMDB0000208
     RDKit          3D
Oxoglutaric acid
 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.9855   -0.2226    1.1813 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5012    0.0535    0.0637 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1185    0.9272   -0.8063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2199   -0.5925   -0.3163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0888    0.1232    0.3883 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2046   -0.4940    0.0347 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2213   -1.4633   -0.7479 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4181    0.0426    0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3955    1.0238    1.3995 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6800   -0.5008    0.3073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8048    1.8750   -0.9766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1165   -0.5163   -1.4078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1795   -1.6521    0.0249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0949    1.1980    0.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1801    0.0991    1.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3703    0.0992   -0.1220 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  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
 10 16  1  0
M  END
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3D SDF for #<Metabolite:0x00007f46c5579488>

HMDB01645_MOL.mol
  Mrv1652309032023562D          

 10  9  0  0  0  0            999 V2000
    1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.0313    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
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  2 10  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000067

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)CCC(=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)

> <INCHI_KEY>
KPGXRSRHYNQIFN-UHFFFAOYSA-N

> <FORMULA>
C5H6O5

> <MOLECULAR_WEIGHT>
146.0981

> <EXACT_MASS>
146.021523302

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
12.166536450524555

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-oxopentanedioic acid

> <ALOGPS_LOGP>
-0.60

> <JCHEM_LOGP>
-0.1092632996666667

> <ALOGPS_LOGS>
-0.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.866108156790311

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.663960637840809

> <JCHEM_PKA_STRONGEST_BASIC>
-9.667717541536742

> <JCHEM_POLAR_SURFACE_AREA>
91.66999999999999

> <JCHEM_REFRACTIVITY>
28.883000000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.31e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
oxoglutarate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f46c5579488>

HMDB0000208
     RDKit          3D
Oxoglutaric acid
 16 15  0  0  0  0  0  0  0  0999 V2000
   -2.9855   -0.2226    1.1813 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5012    0.0535    0.0637 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1185    0.9272   -0.8063 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2199   -0.5925   -0.3163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0888    0.1232    0.3883 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2046   -0.4940    0.0347 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2213   -1.4633   -0.7479 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4181    0.0426    0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3955    1.0238    1.3995 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6800   -0.5008    0.3073 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8048    1.8750   -0.9766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1165   -0.5163   -1.4078 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1795   -1.6521    0.0249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0949    1.1980    0.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1801    0.0991    1.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3703    0.0992   -0.1220 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  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
 10 16  1  0
M  END
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PDB for #<Metabolite:0x00007f46c5579488>

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: HMDB01645_MOL.mol                                 
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0       2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334   0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667  -1.925   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.001   0.385   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.667  -1.925   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -4.001   0.385   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334   1.925   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    8    9                                                  
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
CONECT   10    2                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00007f46c5579488>

COMPND    HMDB0000208
HETATM    1  O1  UNL     1      -2.986  -0.223   1.181  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.501   0.054   0.064  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.118   0.927  -0.806  1.00  0.00           O  
HETATM    4  C2  UNL     1      -1.220  -0.592  -0.316  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.089   0.123   0.388  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.205  -0.494   0.035  1.00  0.00           C  
HETATM    7  O3  UNL     1       1.221  -1.463  -0.748  1.00  0.00           O  
HETATM    8  C5  UNL     1       2.418   0.043   0.606  1.00  0.00           C  
HETATM    9  O4  UNL     1       2.395   1.024   1.400  1.00  0.00           O  
HETATM   10  O5  UNL     1       3.680  -0.501   0.307  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.805   1.875  -0.977  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.117  -0.516  -1.408  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.179  -1.652   0.025  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.095   1.198   0.088  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.180   0.099   1.477  1.00  0.00           H  
HETATM   16  H6  UNL     1       4.370   0.099  -0.122  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   12   13
CONECT    5    6   14   15
CONECT    6    7    7    8
CONECT    8    9    9   10
CONECT   10   16
END
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SMILES for #<Metabolite:0x00007f46c5579488>

OC(=O)CCC(=O)C(O)=O
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INCHI for #<Metabolite:0x00007f46c5579488>

InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
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Synonyms
ValueSource
2-Ketoglutaric acidChEBI
alpha-Ketoglutaric acidChEBI
2-KetoglutarateGenerator
a-KetoglutarateGenerator
a-Ketoglutaric acidGenerator
alpha-KetoglutarateGenerator
Α-ketoglutarateGenerator
Α-ketoglutaric acidGenerator
OxoglutarateGenerator
2-oxo-1,5-PentanedioateHMDB
2-oxo-1,5-Pentanedioic acidHMDB
2-OxoglutarateHMDB
2-Oxoglutaric acidHMDB
2-OxopentanedioateHMDB
2-Oxopentanedioic acidHMDB
alpha-OxoglutarateHMDB
Oxogluric acidHMDB
2 Oxoglutaric acidHMDB
Ketoglutaric acidHMDB
alpha Ketoglutaric acidHMDB
2 Ketoglutaric acidHMDB
alpha KetoglutarateHMDB
alpha OxoglutarateHMDB
2 KetoglutarateHMDB
2 OxoglutarateHMDB
alpha-Oxoglutaric acidHMDB
alpha-Oxopentanedioic acidHMDB
alpha-Keto-glutaric acidHMDB
Α-oxoglutaric acidHMDB
Α-oxopentanedioic acidHMDB
Α-keto-glutaric acidHMDB
Molecular FormulaC5H6O5
Average Mass146.0981
Monoisotopic Mass146.021523302
IUPAC Name2-oxopentanedioic acid
Traditional Nameoxoglutarate
CAS Registry Number328-50-7
SMILES
OC(=O)CCC(=O)C(O)=O
InChI Identifier
InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChI KeyKPGXRSRHYNQIFN-UHFFFAOYSA-N