Np mrd loader

Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:13:39 UTC
NP-MRD IDNP0000203
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-2-Hydroxyglutaric acid
DescriptionL-2-Hydroxyglutaric acid is a metabolite that accumulates in L-2-hydroxyglutaric aciduria, which is 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 ). In humans, 2-hydroxyglutarate is formed by a hydroxyacid-oxoacid transhydrogenase whereas in bacteria it is formed by a 2-hydroxyglutarate synthase. L-2-Hydroxyglutaric acid can be converted to alpha-ketoglutaric acid through the action of 2-hydroxyglutarate dehydrogenase (EC 1.1.99.2). In humans, there are two such enzymes (D2HGDH and L2HGDH). Both the D and L stereoisomers of hydroxyglutaric acid are found in body fluids. L-2-Hydroxyglutaric acid can also be produced via gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). IDH is part of the TCA cycle and this compound is generated in high abundance when IDH is mutated. Since L-2-hydroxyglutaric acid is sufficiently similar in structure to 2-oxoglutarate (2OG), 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-inducible factor (HIF)-mediated hypoxic response and alterations in gene expression through global epigenetic remodeling. The net effect is that L-2-hydroxyglutaric acid causes a cascading effect that leads genetic perturbations and malignant transformation. Depending on the circumstances, L-2-hydroxyglutaric acid can function as an oncometabolite, a neurotoxin, an acidogen, and a metabotoxin. An oncometabolite is a compound that promotes tumour growth and survival. A neurotoxin is compound that is toxic to neurons or neural tissue. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. As an oncometabolite, L-2-hydroxyglutaric acid is a competitive inhibitor of multiple alpha-ketoglutarate-dependent dioxygenases, including histone demethylases and the TET family of 5mC hydroxylases. As a result, high levels of 2-hydroxyglutarate lead to genome-wide histone and DNA methylation alterations, which in turn lead to mutations that ultimately cause cancer (PMID: 29038145 ). As a neurotoxin, L-2-hydroxyglutaric acid mediates its neurotoxicity through activation of N-methyl-D-aspartate receptors. L-2-Hydroxyglutaric acid is structurally similar to the excitatory amino acid glutamate and stimulates neurodegeneration by mechanisms similar to glutamate, NMDA, or mitochondrial toxins (PMID: 12153528 ). As an acidogen, L-2-hydroxyglutaric acid is classified as an alpha hydroxy acid belonging to the general class of compounds known as organic acids. Chronically high levels of L-2-hydroxyglutaric acid are characteristic of the inborn error of metabolism called L-2-hydroxyglutaric aciduria. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart abnormalities, kidney abnormalities, liver damage, seizures, coma, and possibly death. These are the symptoms typical of untreated L-2-hydroxyglutaric aciduria. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures.
Structure
Thumb
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 Mass148.1140 Da
Monoisotopic Mass148.03717 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)Varshavi.d262021-08-30View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Varshavi.d262021-08-30View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)Varshavi.d262021-07-28View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Homo sapiensLOTUS Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
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 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity29.63 m³·mol⁻¹ChemAxon
Polarizability12.97 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000694
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDNot Available
References
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 ]
  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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:9453028 ]
  7. Collins RRJ, Patel K, Putnam WC, Kapur P, Rakheja D: Oncometabolites: A New Paradigm for Oncology, Metabolism, and the Clinical Laboratory. Clin Chem. 2017 Dec;63(12):1812-1820. doi: 10.1373/clinchem.2016.267666. Epub 2017 Oct 16. [PubMed:29038145 ]
  8. Kolker S, Pawlak V, Ahlemeyer B, Okun JG, Horster F, Mayatepek E, Krieglstein J, Hoffmann GF, Kohr G: NMDA receptor activation and respiratory chain complex V inhibition contribute to neurodegeneration in d-2-hydroxyglutaric aciduria. Eur J Neurosci. 2002 Jul;16(1):21-8. [PubMed:12153528 ]