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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-17 00:27:29 UTC
HMDB IDHMDB00694
Secondary Accession NumbersNone
Metabolite Identification
Common NameL-2-Hydroxyglutaric acid
DescriptionL-2-Hydroxyglutaric acid is a metabolite that accumulates in L-2-hydroxyglutaric aciduria (a neurometabolic disorder, OMIM 236792 ), and has been reported in multiple patients who have a clinical phenotype of progressive neurodegeneration with extrapyramidal and cerebellar signs, seizures, and spongiform changes in the white matter (OMIM 600721 ). L-2-hydroxyglutarate can be converted to α-ketoglutaric acid through the action of L-2-hydroxyglutarate dehydrogenase (L2HGDH). L-2-Hydroxyglutaric acid is also considered to be an oncometabolite (or cancer-causing metabolite). It can be produced via gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). IDH is part of TCA cycle and this compound is generated in high abundance when IDH is mutated. L-2-hydroxyglutarate is sufficiently similar in structure to 2-oxogluratate (2OG) that it is able to inhibit a range of 2OG-dependent dioxygenases, including histone lysine demethylases (KDMs) and members of the ten-eleven translocation (TET) family of 5-methylcytosine (5mC) hydroxylases. This inhibitory effect leads to alterations in the hypoxia induced factor (HIF)-mediated hypoxic response and alterations in gene expression through global epigenetic remodeling. The net effect is that L-2-hydroxyglutarate causes a cascading effect that leads genetic perturbations and malignant transformation.
Structure
Thumb
Synonyms
ValueSource
(R)-2-HydroxyglutarateChEBI
(R)-HydroxyglutarateChEBI
(R)-2-Hydroxyglutaric acidGenerator
(2R)-2-HydroxypentanedioateGenerator
(R)-Hydroxyglutaric acidGenerator
(R)-2-Hydroxy-pentanedioateHMDB
(R)-2-Hydroxy-pentanedioic acidHMDB
(R)-a-HydroxyglutarateHMDB
(R)-a-Hydroxyglutaric acidHMDB
(R)-alpha-HydroxyglutarateHMDB
(R)-alpha-Hydroxyglutaric acidHMDB
2-Hydroxy-D-glutarateHMDB
2-Hydroxy-D-glutaric acidHMDB
2-Hydroxy-delta-glutarateHMDB
2-Hydroxy-delta-glutaric acidHMDB
D-2-HydroxyglutarateHMDB
D-a-HydroxyglutarateHMDB
D-a-Hydroxyglutaric acidHMDB
delta-2-HydroxyglutarateHMDB
delta-2-Hydroxyglutaric acidHMDB
delta-alpha-HydroxyglutarateHMDB
delta-alpha-Hydroxyglutaric acidHMDB
Chemical FormulaC5H8O5
Average Molecular Weight148.114
Monoisotopic Molecular Weight148.037173366
IUPAC Name(2R)-2-hydroxypentanedioic acid
Traditional NameD-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 KeyInChIKey=HWXBTNAVRSUOJR-VKHMYHEASA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Monosaccharide
  • Hydroxy acid
  • Dicarboxylic acid or derivatives
  • Alpha-hydroxy acid
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Butanoate metabolism
ApplicationNot Available
Cellular locations
  • Cytoplasm (predicted from logP)
  • Mitochondria
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility157.0 mg/mLALOGPS
logP-1ALOGPS
logP-0.82ChemAxon
logS0.03ALOGPS
pKa (Strongest Acidic)3.28ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity29.63 m3·mol-1ChemAxon
Polarizability12.97 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
  • Mitochondria
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1.5 (0.0-1.5) uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified1 uMChildren (1-13 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified1.0 +/- 1.0 uMAdult (>18 years old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot ApplicableNot SpecifiedNot Specified
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
    • Zerihun T. Dame, ...
details
UrineDetected and Quantified24.379 +/- 9.126 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Mordechai, Hien, ...
details
UrineDetected and Quantified51.9 (13.7-97.3) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified41.5 (14.6-150.3) umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected but not QuantifiedNot ApplicableAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified12.4 (5.1-24.9) umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected and Quantified11.2 (4.6-33.6) umol/mmol creatinineAdolescent (13-18 years old)BothNormal details
UrineDetected and Quantified2.2 (0.8-52) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified<26.15 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
details
UrineDetected and Quantified33.0 (13.3-77.9) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
UrineDetected and Quantified33.0 (20.0-46.0) umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified47.0 +/- 13.0 uMAdult (>18 years old)BothL-2-hydroxyglutaric aciduria details
BloodDetected and Quantified0.75 (0.0-1.5) uMAdult (>18 years old)Both2-hydroxyglutaric aciduria details
BloodDetected and Quantified33.3 (7.0-61.0) uMChildren (1-13 years old)BothL-2-hydroxyglutaric aciduria details
UrineDetected and Quantified61.074 +/- 36.982 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Mordechai, Hien, ...
details
UrineDetected and Quantified50.00-4300.00 umol/mmol creatinineChildren (1-13 years old)BothD, L-2-hydroxyglutaric aciduria details
Associated Disorders and Diseases
Disease References
2-hydroxyglutaric aciduria
  1. MetaGene [Link]
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. [8134166 ]
D, L-2-hydroxygluraric aciduria
  1. MetaGene [Link]
Associated OMIM IDs
  • 236792 (L-2-hydroxyglutaric aciduria)
  • 236792 (2-hydroxyglutaric aciduria)
  • 615182 (D, L-2-hydroxygluraric aciduria)
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022185
KNApSAcK IDNot Available
Chemspider ID388969
KEGG Compound IDC03196
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
NuGOwiki LinkHMDB00694
Metagene LinkHMDB00694
METLIN ID5662
PubChem Compound439939
PDB IDS2G
ChEBI ID32797
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)Download (PDF)
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. [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. [8134166 ]
  3. Rashed MS, AlAmoudi M, Aboul-Enein HY: Chiral liquid chromatography tandem mass spectrometry in the determination of the configuration of 2-hydroxyglutaric acid in urine. Biomed Chromatogr. 2000 Aug;14(5):317-20. [10960831 ]
  4. Fujitake J, Ishikawa Y, Fujii H, Nishimura K, Hayakawa K, Inoue F, Terada N, Okochi M, Tatsuoka Y: L-2-hydroxyglutaric aciduria: two Japanese adult cases in one family. J Neurol. 1999 May;246(5):378-82. [10399870 ]
  5. Barth PG, Hoffmann GF, Jaeken J, Lehnert W, Hanefeld F, van Gennip AH, Duran M, Valk J, Schutgens RB, Trefz FK, et al.: L-2-hydroxyglutaric acidemia: a novel inherited neurometabolic disease. Ann Neurol. 1992 Jul;32(1):66-71. [1642474 ]
  6. de Klerk JB, Huijmans JG, Stroink H, Robben SG, Jakobs C, Duran M: L-2-hydroxyglutaric aciduria: clinical heterogeneity versus biochemical homogeneity in a sibship. Neuropediatrics. 1997 Dec;28(6):314-7. [9453028 ]

Enzymes

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