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Showing metabocard for L-2-Hydroxyglutaric acid (HMDB0000694)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-03-07 02:49:05 UTC
HMDB IDHMDB0000694
Secondary Accession Numbers
  • HMDB00694
Metabolite Identification
Common NameL-2-Hydroxyglutaric acid
Description
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000694 (L-2-Hydroxyglutaric acid)

  Mrv1652305271900172D          

 10  9  0  0  0  0            999 V2000
 9998.6124 9997.7078    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9997.8979 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1831 9997.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4684 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.7534 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4684 9998.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3301 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0437 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3301 9998.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6124 9996.8823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 10  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for HMDB0000694 (L-2-Hydroxyglutaric acid)

HMDB0000694
     RDKit          3D
L-2-Hydroxyglutaric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
    1.9977   -0.2899   -1.4646 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1686    0.1066   -0.3001 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4952    0.0307    0.1750 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1853    0.6390    0.6379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2303    0.6592    0.2044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8392   -0.6798   -0.0787 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2355   -1.4124   -1.0744 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3010   -0.5240   -0.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7416   -1.0283   -1.4581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0707    0.1863    0.4926 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6610   -0.4993    1.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2910    0.0467    1.6018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5412    1.6852    0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4219    1.3837   -0.6309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8187    1.1009    1.0675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8160   -1.3288    0.8399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6126   -1.2382   -1.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2525    1.1624    0.4668 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  1  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
  6 16  1  1
  7 17  1  0
 10 18  1  0
M  END
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3D SDF for HMDB0000694 (L-2-Hydroxyglutaric acid)

  Mrv1652305271900172D          

 10  9  0  0  0  0            999 V2000
 9998.6124 9997.7078    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9997.8979 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1831 9997.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4684 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.7534 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4684 9998.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3301 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0437 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3301 9998.9448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6124 9996.8823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 10  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000694

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m0/s1

> <INCHI_KEY>
HWXBTNAVRSUOJR-VKHMYHEASA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173366

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.9730498807228

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-hydroxypentanedioic acid

> <ALOGPS_LOGP>
-1.04

> <JCHEM_LOGP>
-0.824980223

> <ALOGPS_LOGS>
0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.159324461588801

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.276485914460605

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8068384384876675

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
29.6302

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.57e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-2-hydroxyglutaric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000694 (L-2-Hydroxyglutaric acid)

HMDB0000694
     RDKit          3D
L-2-Hydroxyglutaric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
    1.9977   -0.2899   -1.4646 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1686    0.1066   -0.3001 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4952    0.0307    0.1750 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1853    0.6390    0.6379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2303    0.6592    0.2044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8392   -0.6798   -0.0787 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2355   -1.4124   -1.0744 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3010   -0.5240   -0.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7416   -1.0283   -1.4581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0707    0.1863    0.4926 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6610   -0.4993    1.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2910    0.0467    1.6018 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5412    1.6852    0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4219    1.3837   -0.6309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8187    1.1009    1.0675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8160   -1.3288    0.8399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6126   -1.2382   -1.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2525    1.1624    0.4668 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  1  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
  6 16  1  1
  7 17  1  0
 10 18  1  0
M  END
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PDB for HMDB0000694 (L-2-Hydroxyglutaric acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0    8664.0768662.388   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8662.7438663.157   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8661.4088662.388   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8660.0748663.157   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8658.7408662.388   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8660.0748664.697   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8665.4168663.157   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8666.7488662.388   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8665.4168664.697   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8664.0768660.847   0.000  0.00  0.00           O+0
CONECT    1    2    7   10                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    1                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0000694 (L-2-Hydroxyglutaric acid)

COMPND    HMDB0000694
HETATM    1  O1  UNL     1       1.998  -0.290  -1.465  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.169   0.107  -0.300  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.495   0.031   0.175  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.185   0.639   0.638  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.230   0.659   0.204  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.839  -0.680  -0.079  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.235  -1.412  -1.074  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.301  -0.524  -0.411  1.00  0.00           C  
HETATM    9  O4  UNL     1      -2.742  -1.028  -1.458  1.00  0.00           O  
HETATM   10  O5  UNL     1      -3.071   0.186   0.493  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.661  -0.499   1.007  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.291   0.047   1.602  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.541   1.685   0.901  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.422   1.384  -0.631  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.819   1.101   1.067  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.816  -1.329   0.840  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.613  -1.238  -1.975  1.00  0.00           H  
HETATM   18  H8  UNL     1      -3.253   1.162   0.467  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    8   16
CONECT    7   17
CONECT    8    9    9   10
CONECT   10   18
END
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SMILES for HMDB0000694 (L-2-Hydroxyglutaric acid)

O[C@@H](CCC(O)=O)C(O)=O
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INCHI for HMDB0000694 (L-2-Hydroxyglutaric acid)

InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(S)-2-HydroxyglutarateChEBI
(S)-2-Hydroxyglutaric acidGenerator
L-2-HydroxyglutarateGenerator
(S)-Α-hydroxyglutarateHMDB
(S)-Α-hydroxyglutaric acidHMDB
(S)-alpha-HydroxyglutarateHMDB
(S)-alpha-Hydroxyglutaric acidHMDB
2-Hydroxy-(S)-pentanedioateHMDB
2-Hydroxy-(S)-pentanedioic acidHMDB
2-Hydroxy-L-glutarateHMDB
2-Hydroxy-L-glutaric acidHMDB
L-Α-hydroxyglutarateHMDB
L-Α-hydroxyglutaric acidHMDB
L-alpha-HydroxyglutarateHMDB
L-alpha-Hydroxyglutaric acidHMDB
L-2-Hydroxyglutaric acidHMDB
Chemical FormulaC5H8O5
Average Molecular Weight148.114
Monoisotopic Molecular Weight148.037173366
IUPAC Name(2S)-2-hydroxypentanedioic acid
Traditional NameL-2-hydroxyglutaric acid
CAS Registry Number13095-48-2
SMILES
O[C@@H](CCC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m0/s1
InChI KeyHWXBTNAVRSUOJR-VKHMYHEASA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain hydroxy acids and derivatives. These are hydroxy acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassShort-chain hydroxy acids and derivatives
Direct ParentShort-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Short-chain hydroxy acid
  • Fatty acid
  • Monosaccharide
  • Dicarboxylic acid or derivatives
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Indirect biological roleBiological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available119.063http://allccs.zhulab.cn/database/detail?ID=AllCCS00000025
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
  • Mitochondria
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
L-2-Hydroxyglutaric aciduria
  1. Gibson KM, ten Brink HJ, Schor DS, Kok RM, Bootsma AH, Hoffmann GF, Jakobs C: Stable-isotope dilution analysis of D- and L-2-hydroxyglutaric acid: application to the detection and prenatal diagnosis of D- and L-2-hydroxyglutaric acidemias. Pediatr Res. 1993 Sep;34(3):277-80. [PubMed:8134166 ]
  2. Seijo-Martinez M, Navarro C, Castro del Rio M, Vila O, Puig M, Ribes A, Butron M: L-2-hydroxyglutaric aciduria: clinical, neuroimaging, and neuropathological findings. Arch Neurol. 2005 Apr;62(4):666-70. [PubMed:15824270 ]
  3. Gibson KM, Craigen W, Herman GE, Jakobs C: D-2-hydroxyglutaric aciduria in a newborn with neurological abnormalities: a new neurometabolic disorder? J Inherit Metab Dis. 1993;16(3):497-500. [PubMed:7609436 ]
  4. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
D, L-2-hydroxyglutaric aciduria
  1. Kranendijk M, Struys EA, Salomons GS, Van der Knaap MS, Jakobs C: Progress in understanding 2-hydroxyglutaric acidurias. J Inherit Metab Dis. 2012 Jul;35(4):571-87. doi: 10.1007/s10545-012-9462-5. Epub 2012 Mar 6. [PubMed:22391998 ]
  2. Gibson KM, Craigen W, Herman GE, Jakobs C: D-2-hydroxyglutaric aciduria in a newborn with neurological abnormalities: a new neurometabolic disorder? J Inherit Metab Dis. 1993;16(3):497-500. [PubMed:7609436 ]
  3. Muntau AC, Roschinger W, Merkenschlager A, van der Knaap MS, Jakobs C, Duran M, Hoffmann GF, Roscher AA: Combined D-2- and L-2-hydroxyglutaric aciduria with neonatal onset encephalopathy: a third biochemical variant of 2-hydroxyglutaric aciduria? Neuropediatrics. 2000 Jun;31(3):137-40. doi: 10.1055/s-2000-7497. [PubMed:10963100 ]
  4. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
D-2-hydroxyglutaric aciduria
  1. Wajne M, Vargas CR, Funayama C, Fernandez A, Elias ML, Goodman SI, Jakobs C, van der Knaap MS: D-2-Hydroxyglutaric aciduria in a patient with a severe clinical phenotype and unusual MRI findings. J Inherit Metab Dis. 2002 Feb;25(1):28-34. [PubMed:11999977 ]
Associated OMIM IDs
  • 236792 (L-2-Hydroxyglutaric aciduria)
  • 615182 (D, L-2-hydroxyglutaric aciduria)
  • 610247 (Eosinophilic esophagitis)
  • 600721 (D-2-hydroxyglutaric aciduria)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022185
KNApSAcK IDNot Available
Chemspider ID388969
KEGG Compound IDC03196
BioCyc IDCPD-381
BiGG IDNot Available
Wikipedia LinkAlpha-Hydroxyglutaric acid
METLIN IDNot Available
PubChem Compound439939
PDB IDNot Available
ChEBI ID32797
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000222
Good Scents IDNot Available
References
Synthesis ReferenceKobayashi, Hidehiko; Yamaguchi, Koretaka; Yamashita, Takeshi. a-Hydroxyglutaric acid from glutamic acid. Jpn. Tokkyo Koho (1968), 3 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
  2. Gibson KM, ten Brink HJ, Schor DS, Kok RM, Bootsma AH, Hoffmann GF, Jakobs C: Stable-isotope dilution analysis of D- and L-2-hydroxyglutaric acid: application to the detection and prenatal diagnosis of D- and L-2-hydroxyglutaric acidemias. Pediatr Res. 1993 Sep;34(3):277-80. [PubMed:8134166 ]
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Enzymes

Enzyme Details
1. L-2-hydroxyglutarate dehydrogenase, mitochondrial
General function:
Involved in 2-hydroxyglutarate dehydrogenase activity
Specific function:
Not Available
Gene Name:
L2HGDH
Uniprot ID:
Q9H9P8
Molecular weight:
50315.58
Reactions
L-2-Hydroxyglutaric acid + acceptor → Oxoglutaric acid + reduced acceptordetails