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Human Metabolome Database Version 2.5

 

Showing metabocard for L-2-Hydroxyglutaric acid (HMDB00694)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2005-11-16 15:48:42
Update Date 2011-12-30 15:48:05
Accession Number HMDB00694
Secondary Accession Numbers Not Available
Common Name L-2-Hydroxyglutaric acid
Description L-2-Hydroxyglutaric acid is a metabolite that accumulates in D-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) and Spondyloenchondrodysplasia (OMIM 271550).
Synonyms
  1. (S)-2-Hydroxyglutarate
  2. (S)-2-Hydroxyglutaric acid
  3. (S)-a-Hydroxyglutarate
  4. (S)-a-Hydroxyglutaric acid
  5. 2-hydroxy-(S)-Pentanedioate
  6. 2-hydroxy-(S)-Pentanedioic acid
  7. 2-hydroxy-L-Glutarate
  8. 2-hydroxy-L-Glutaric acid
  9. L-2-Hydroxyglutarate
  10. L-a-Hydroxyglutarate
  11. L-a-Hydroxyglutaric acid
  12. (S)-alpha-Hydroxyglutarate
  13. (S)-alpha-Hydroxyglutaric acid
  14. L-alpha-Hydroxyglutarate
  15. L-alpha-Hydroxyglutaric acid
Chemical IUPAC Name (2S)-2-hydroxypentanedioic acid
Chemical Formula C5H8O5
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Organic acids
Class
  • Dicarboxylic Acids
Sub Class
  • Short chain dicarboxylic acids
Family
  • Mammalian Metabolite
Species
  • secondary alcohol
  • carboxylic acid
  • alpha-hydroxyacid
Biofunction
  • Component of Butanoate metabolism
Application
Source
  • Endogenous
Average Molecular Weight 148.114
Monoisotopic Molecular Weight 148.037170
Isomeric SMILES O[C@@H](CCC(O)=O)C(O)=O
Canonical SMILES OC(CCC(O)=O)C(O)=O
KEGG Compound ID C03196 Link Image
BioCyc ID Not Available
BiGG ID Not Available
Wikipedia Link Not Available
NuGOwiki Link HMDB00694 Link Image
Metagene Link HMDB00694 Link Image
METLIN ID 5662 Link Image
PubChem Compound 439939 Link Image
PubChem Substance 6073 Link Image
ChEBI ID Not Available
CAS Registry Number 13095-48-2
InChI Identifier InChI=1/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m0/s1
Synthesis Reference Kobayashi, Hidehiko; Yamaguchi, Koretaka; Yamashita, Takeshi. a-Hydroxyglutaric acid from glutamic acid. Jpn. Tokkyo Koho (1968), 3 pp.
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 157.0 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge -2
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -1.04 [Predicted by ALOGPS]; -1.1 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show Link Image
SDF File Show Link Image
PDB File Show Link Image
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Download Spectrum
Download FID (Varian)
Show Experimental Conditions Link Image
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Download Spectrum
Download FID (Bruker)
Show Experimental Conditions Link Image
Predicted 1H NMR Spectrum Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
Show Peaklist
Mass Spectrum
Low Energy
Download File
Show Experimental Conditions Link Image
Medium Energy
Download File
Show Experimental Conditions Link Image
High Energy
Download File
Show Experimental Conditions Link Image
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • Cytoplasm (Predicted from LogP)
Biofluid Location
  • Blood
  • Cerebrospinal Fluid
  • Urine
Tissue Location Not Available
Concentrations (Normal)
Biofluid Blood
Value 1.5 (0.0-1.5) uM
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Hoffmann GF, Meier-Augenstein W, Stockler S, Surtees R, Rating D, Nyhan WL: Physiology and pathophysiology of organic acids in cerebrospinal fluid. J Inherit Metab Dis. 1993;16(4):648-69. [PubMed Link Image]
Biofluid CSF
Value 1.0 +/- 1.0 uM
Age Adult:>18 yrs old
Sex N/A
Patient information Normal
Comments Not Available
References
  • Hoffmann GF, Meier-Augenstein W, Stockler S, Surtees R, Rating D, Nyhan WL: Physiology and pathophysiology of organic acids in cerebrospinal fluid. J Inherit Metab Dis. 1993;16(4):648-69. [PubMed Link Image]
Biofluid CSF
Value 1 uM
Age Children:1-13 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Hoffmann GF, Meier-Augenstein W, Stockler S, Surtees R, Rating D, Nyhan WL: Physiology and pathophysiology of organic acids in cerebrospinal fluid. J Inherit Metab Dis. 1993;16(4):648-69. [PubMed Link Image]
Biofluid Urine
Value 51.9 (13.7-97.3) umol/mmol creatinine
Age Newborn:0-30 days old
Sex Both
Patient information Normal
Comments Not Available
References
  • 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 Link Image]
Biofluid Urine
Value 41.5 (14.6-150.3) umol/mmol creatinine
Age Infant:0-1 yr old
Sex Both
Patient information Normal
Comments Not Available
References
  • 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 Link Image]
Biofluid Urine
Value 12.4 (5.1-24.9) umol/mmol creatinine
Age Children:1-13 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • 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 Link Image]
Biofluid Urine
Value 11.2 (4.6-33.6) umol/mmol creatinine
Age Adolescent:13-18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • 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 Link Image]
Biofluid Urine
Value 33.0 (20.0-46.0) umol/mmol creatinine
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Metagene: 2-HYDROXYGLUTARIC ACIDEMIA (L)
Concentrations (Abnormal)
Biofluid Blood
Value 47.0 +/- 13.0 uM
Age Adult:>18 yrs old
Sex Both
Condition L-2-hydroxyglutaric aciduria
Comments Not Available
References
  • 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 Link Image]
Biofluid Blood
Value 0.75 (0.0-1.5) uM
Age Adult:>18 yrs old
Sex Both
Condition 2-hydroxyglutaric aciduria
Comments Not Available
References
Biofluid Blood
Value 33.3 (7.0-61.0) uM
Age Adult:>18 yrs old
Sex Both
Condition 2-hydroxyglutaric aciduria
Comments Not Available
References
Biofluid Urine
Value 50.00-4300.00 umol/mmol creatinine
Age Adult:>18 yrs old
Sex Both
Condition 2-hydroxyglutaric aciduria
Comments Not Available
References
  • Metagene: 2-HYDROXYGLUTARIC ACIDEMIA (L)
Associated Disorders
Condition References
2-hydroxyglutaric aciduria
L-2-hydroxyglutaric aciduria
  • 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 Link Image]
OMIM ID
  • 236792 Link Image (2-hydroxyglutaric aciduria)
  • 236792 Link Image (L-2-hydroxyglutaric aciduria)
Pathways 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 Link Image]
  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 Link Image]
  3. 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 Link Image]
  4. 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 Link Image]
  5. 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 Link Image]
  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 Link Image]
Metabolic Enzymes
  1. L-2-hydroxyglutarate dehydrogenase, mitochondrial
Enzyme 1 [top]
Enzyme 1 ID 7987
Enzyme 1 Name L-2-hydroxyglutarate dehydrogenase, mitochondrial
Enzyme 1 Synonyms
  1. Duranin
Enzyme 1 Gene Name L2HGDH
Enzyme 1 Protein Sequence >L-2-hydroxyglutarate dehydrogenase, mitochondrial
MVPALRYLVGACGRARGRFAGGSPGACGFASGRPRPLCGGSRSASTSSFDIVIVGGGIVG
LASARALILRHPSLSIGVLEKEKDLAVHQTGHNSGVIHSGIYYKPESLKAKLCVQGAALL
YEYCQQKGISYKQCGKLIVAVEQEEIPRLQALYEKGLQNGVPGLRLIQQEDIKKKEPYCR
GLMAIDCPHTGIVDYRQVALSFAQDFQEAGGSVLTNFEVKGIEMAKESPSRSIDGMQYPI
VIKNTKGEEIRCQYVVTCAGLYSDRISELSGCTPDPRIVPFRGDYLLLKPEKCYLVKGNI
YPVPDSRFPFLGVHFTPRMDGSIWLGPNAVLAFKREGYRPFDFSATDVMDIIINSGLIKL
ASQNFSYGVTEMYKACFLGATVKYLQKFIPEITISDILRGPAGVRAQALDRDGNLVEDFV
FDAGVGDIGNRILHVRNAPSPAATSSIAISGMIADEVQQRFEL
Enzyme 1 Number of Residues 463
Enzyme 1 Molecular Weight 50358.6
Enzyme 1 Theoretical pI 8.34
Enzyme 1 GO Classification
Function
  • catalytic activity
  • oxidoreductase activity
Process
Component
Enzyme 1 General Function Involved in 2-hydroxyglutarate dehydrogenase activity
Enzyme 1 Specific Function (S)-2-hydroxyglutarate + acceptor = 2- oxoglutarate + reduced acceptor
Enzyme 1 Pathways
Enzyme 1 Reactions
  • (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor [RN:R00298]
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • None
Enzyme 1 Transmembrane Regions
  • None
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 10434215 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID Q9H9P8 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name L2HDH_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1392 bp
ATGGTGCCAGCGCTGCGTTATTTGGTTGGTGCCTGCGGACGGGCCCGCGGGCTTTTCGCC
GGTGGCTCCCCTGGGGCGTGCGGGTTCGCGTCTGGGAGGCCAAGACCGCTGTGTGGAGGT
AGCCGCAGCGCCAGCACCAGCTCATTTGATATAGTCATCGTTGGTGGCGGAATTGTGGGG
CTTGCCTCTGCCAGAGCACTCATCCTGCGACATCCATCACTTTCTATTGGTGTTCTGGAA
AAGGAGAAAGATTTAGCTGTTCACCAGACTGGACATAACAGTGGTGTCATACATAGTGGA
ATTTATTATAAACCTGAGTCTCTGAAAGCCAAATTATGTGTACAAGGTGCAGCCCTCCTC
TATGAGTACTGTCAGCAAAAGGGGATTTCCTACAAGCAGTGTGGCAAGCTTATAGTAGCT
GTTGAACAAGAAGAAATTCCCAGACTTCAGGCCCTATATGAGAAAGGCCTCCAGAATGGT
GTCCCGGGCCTGAGGCTGATCCAGCAGGAGGATATAAAAAAGAAGGAGCCATATTGTAGG
GGTCTAATGGCTATTGATTGTCCACATACTGGCATTGTGGACTATCGGCAGGTGGCTTTG
TCATTTGCCCAGGATTTCCAAGAAGCAGGTGGCTCTGTCTTGACCAATTTTGAAGTAAAA
GGTATTGAAATGGCTAAAGAAAGTCCTTCAAGAAGTATAGATGGAATGCAATATCCAATT
GTTATAAAGAATACAAAGGGAGAGGAAATTCGATGTCAGTATGTTGTGACATGTGCAGGA
CTTTACTCAGACCGTATTTCAGAGTTGAGTGGCTGCACTCCTGATCCTCGAATTGTACCA
TTCCGGGGAGATTACCTGCTTTTGAAGCCAGAAAAATGTTATCTTGTAAAAGGAAATATT
TATCCGGTCCCAGATAGCCGGTTTCCTTTCCTAGGAGTTCACTTCACACCAAGGATGGAT
GGCAGTATTTGGCTAGGGCCTAATGCAGTTCTTGCCTTTAAACGAGAGGGTTACAGACCC
TTTGACTTCAGTGCCACAGATGTTATGGATATAATTATCAATAGTGGCTTGATTAAACTG
GCATCCCAGAATTTTTCCTATGGAGTTACTGAAATGTATAAAGCATGTTTTCTTGGTGCA
ACAGTGAAGTATCTTCAAAAATTCATCCCTGAAATTACTATCAGTGATATACTTAGGGGC
CCAGCTGGAGTAAGAGCCCAGGCCCTGGATAGAGATGGAAATCTGGTAGAAGATTTTGTA
TTTGATGCAGGAGTTGGGGATATTGGAAATCGCATTCTTCATGTGAGAAATGCACCTTCT
CCTGCTGCTACTTCTTCCATTGCAATTTCTGGAATGATTGCAGATGAAGTACAACAAAGA
TTTGAATTATAA
Enzyme 1 GenBank Gene ID AK022680 Link Image
Enzyme 1 GeneCard ID L2HGDH Link Image
Enzyme 1 GenAtlas ID Not Available
Enzyme 1 HGNC ID Not Available
Enzyme 1 Chromosome Location 1
Enzyme 1 Locus 14q21.3
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Rzem R, Veiga-da-Cunha M, Noel G, Goffette S, Nassogne MC, Tabarki B, Scholler C, Marquardt T, Vikkula M, Van Schaftingen E: A gene encoding a putative FAD-dependent L-2-hydroxyglutarate dehydrogenase is mutated in L-2-hydroxyglutaric aciduria. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16849-54. Epub 2004 Nov 17. [PubMed Link Image]
  2. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, Sugano S: Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet. 2004 Jan;36(1):40-5. Epub 2003 Dec 21. [PubMed Link Image]
  3. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed Link Image]
  4. Rzem R, Van Schaftingen E, Veiga-da-Cunha M: The gene mutated in l-2-hydroxyglutaric aciduria encodes l-2-hydroxyglutarate dehydrogenase. Biochimie. 2006 Jan;88(1):113-6. Epub 2005 Jun 23. [PubMed Link Image]
  5. Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M: Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science. 2009 Aug 14;325(5942):834-40. Epub 2009 Jul 16. [PubMed Link Image]
  6. Topcu M, Jobard F, Halliez S, Coskun T, Yalcinkayal C, Gerceker FO, Wanders RJ, Prud'homme JF, Lathrop M, Ozguc M, Fischer J: L-2-Hydroxyglutaric aciduria: identification of a mutant gene C14orf160, localized on chromosome 14q22.1. Hum Mol Genet. 2004 Nov 15;13(22):2803-11. Epub 2004 Sep 22. [PubMed Link Image]
  7. Vilarinho L, Cardoso ML, Gaspar P, Barbot C, Azevedo L, Diogo L, Santos M, Carrilho I, Fineza I, Kok F, Chorao R, Alegria P, Martins E, Teixeira J, Cabral Fernandes H, Verhoeven NM, Salomons GS, Santorelli FM, Cabral P, Amorim A, Jakobs C: Novel L2HGDH mutations in 21 patients with L-2-hydroxyglutaric aciduria of Portuguese origin. Hum Mutat. 2005 Oct;26(4):395-6. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available