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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-10-09 20:59:18 UTC
HMDB IDHMDB0000428
Secondary Accession Numbers
  • HMDB00428
Metabolite Identification
Common Name3-Hydroxyglutaric acid
Description3-Hydroxyglutaric acid is a member of the class of compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. 3-Hydroxyglutaric acid is soluble (in water) and a weakly acidic compound (based on its pKa). When present in sufficiently high levels, 3-hydroxyglutaric acid can act as an acidogen and a metabotoxin. 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. Chronically high levels of 3-hydroxyglutaric acid are associated with glutaric aciduria type I (glutaric acidemia type I, glutaryl-CoA dehydrogenase deficiency, GA1, or GAT1). GA1 is an inherited disorder in which the body is unable to completely break down the amino acids lysine, hydroxylysine, and tryptophan due to a deficiency of mitochondrial glutaryl-CoA dehydrogenase (EC 1.3.99.7, GCDH). Excessive levels of their intermediate breakdown products (e.g. glutaric acid, glutaryl-CoA, 3-hydroxyglutaric acid, glutaconic acid) can accumulate and cause damage to the brain (and also other organs), but particularly the basal ganglia. GA1 is associated with a risk for intracranial and retinal hemorrhage, and non-specific white matter changes. Babies with glutaric acidemia type I are often born with unusually large heads (macrocephaly). Other symptoms include spasticity (increased muscle tone/stiffness) and dystonia (involuntary muscle contractions resulting in abnormal movement or posture), but many affected individuals are asymptomatic. Seizures and coma (encephalopathy) are rare. GA1 also causes secondary carnitine deficiency because 3-hydroxyglutaric acid, like other organic acids, is detoxified by carnitine.
Structure
Data?1582752131
Synonyms
ValueSource
3-Hydroxy-glutaric acidChEBI
beta-Hydroxyglutaric acidChEBI
3-Hydroxy-glutarateGenerator
b-HydroxyglutarateGenerator
b-Hydroxyglutaric acidGenerator
beta-HydroxyglutarateGenerator
Β-hydroxyglutarateGenerator
Β-hydroxyglutaric acidGenerator
3-HydroxyglutarateGenerator
3-Hydroxypentanedioic acidHMDB
2,4-Dideoxypentaric acidHMDB
3-HydroxypentanedioateHMDB
3-Hydroxyglutaric acidMeSH
Chemical FormulaC5H8O5
Average Molecular Weight148.114
Monoisotopic Molecular Weight148.037173366
IUPAC Name3-hydroxypentanedioic acid
Traditional Name3-hydroxyglutaric acid
CAS Registry Number638-18-6
SMILES
OC(CC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C5H8O5/c6-3(1-4(7)8)2-5(9)10/h3,6H,1-2H2,(H,7,8)(H,9,10)
InChI KeyZQHYXNSQOIDNTL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassBeta hydroxy acids and derivatives
Direct ParentBeta hydroxy acids and derivatives
Alternative Parents
Substituents
  • Short-chain hydroxy acid
  • Beta-hydroxy acid
  • Fatty acid
  • Dicarboxylic acid or derivatives
  • 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 DescriptorsNot Available
Ontology
Physiological effect

Adverse health effect

Disposition

Biological location

Source

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility172 g/LALOGPS
logP-1.2ALOGPS
logP-1ChemAxon
logS0.06ALOGPS
pKa (Strongest Acidic)3.52ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity29.5 m³·mol⁻¹ChemAxon
Polarizability12.81 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+131.9831661259
DarkChem[M-H]-127.85231661259
AllCCS[M+H]+134.03432859911
AllCCS[M-H]-127.15332859911
DeepCCS[M+H]+123.50630932474
DeepCCS[M-H]-120.04430932474
DeepCCS[M-2H]-156.85130932474
DeepCCS[M+Na]+132.06730932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Hydroxyglutaric acidOC(CC(O)=O)CC(O)=O2439.0Standard polar33892256
3-Hydroxyglutaric acidOC(CC(O)=O)CC(O)=O1097.0Standard non polar33892256
3-Hydroxyglutaric acidOC(CC(O)=O)CC(O)=O1395.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Hydroxyglutaric acid,1TMS,isomer #1C[Si](C)(C)OC(CC(=O)O)CC(=O)O1429.7Semi standard non polar33892256
3-Hydroxyglutaric acid,1TMS,isomer #2C[Si](C)(C)OC(=O)CC(O)CC(=O)O1437.2Semi standard non polar33892256
3-Hydroxyglutaric acid,2TMS,isomer #1C[Si](C)(C)OC(=O)CC(CC(=O)O)O[Si](C)(C)C1502.1Semi standard non polar33892256
3-Hydroxyglutaric acid,2TMS,isomer #2C[Si](C)(C)OC(=O)CC(O)CC(=O)O[Si](C)(C)C1524.4Semi standard non polar33892256
3-Hydroxyglutaric acid,3TMS,isomer #1C[Si](C)(C)OC(=O)CC(CC(=O)O[Si](C)(C)C)O[Si](C)(C)C1586.4Semi standard non polar33892256
3-Hydroxyglutaric acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(CC(=O)O)CC(=O)O1676.5Semi standard non polar33892256
3-Hydroxyglutaric acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)CC(O)CC(=O)O1717.9Semi standard non polar33892256
3-Hydroxyglutaric acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CC(CC(=O)O)O[Si](C)(C)C(C)(C)C1978.4Semi standard non polar33892256
3-Hydroxyglutaric acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC(=O)CC(O)CC(=O)O[Si](C)(C)C(C)(C)C1976.8Semi standard non polar33892256
3-Hydroxyglutaric acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CC(CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2213.7Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0536-9200000000-95922095d2aa1db75f8b2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (3 TMS) - 70eV, Positivesplash10-00gs-9081000000-c273d86d7f22986f4bcd2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxyglutaric acid GC-MS (TBDMS_3_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxyglutaric acid 40V, Negative-QTOFsplash10-0a4l-9000000000-9249b84ab50ffbbbab002021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxyglutaric acid 20V, Negative-QTOFsplash10-0a4i-9100000000-a007a5c975eeaa8942982021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 3-Hydroxyglutaric acid 10V, Negative-QTOFsplash10-0fbi-4900000000-111cef5b8a6a577bf7012021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 10V, Positive-QTOFsplash10-01qa-1900000000-83e00bd7b92b7f2f98322016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 20V, Positive-QTOFsplash10-01qi-5900000000-da4f8a92eae4f7ae9a732016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 40V, Positive-QTOFsplash10-000i-9000000000-a255aedbfaa3bce837b82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 10V, Negative-QTOFsplash10-0002-2900000000-6ea9c60bf78cda297a392016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 20V, Negative-QTOFsplash10-0pbj-9800000000-db9f014d4e5dce1cc78f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 40V, Negative-QTOFsplash10-0a4i-9100000000-89edd1cbe710cf97835d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 10V, Positive-QTOFsplash10-0019-9400000000-3231e946df512b24401a2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 20V, Positive-QTOFsplash10-0076-9200000000-4ffdd7ac7861294da7832021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 40V, Positive-QTOFsplash10-006x-9000000000-f46770ad7298e670b4b72021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 10V, Negative-QTOFsplash10-0f72-5900000000-c4e9005c7c37f89f6fe32021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 20V, Negative-QTOFsplash10-052f-9100000000-de505ca4195705703e192021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxyglutaric acid 40V, Negative-QTOFsplash10-0a4l-9000000000-cae7897ab9482c2d43bc2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2021-10-10Wishart LabView Spectrum
Experimental 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)2021-10-10Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 500 MHz, H2O, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Locations
  • Neuron
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.15 +/- 0.08 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified<0.2 uMNot SpecifiedNot SpecifiedNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.07 +/- 0.03 uMNot SpecifiedNot SpecifiedNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified22-67 uMNot SpecifiedNot SpecifiedNormal details
UrineDetected and Quantified41-44 umol/mmol creatinineNewborn (0-30 days old)Both
Normal
details
UrineDetected and Quantified0-3 umol/mmol creatinineNewborn (0-30 days old)MaleNormal details
UrineDetected and Quantified<11.51 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1.8 uMNewborn (0-30 days old)MaleGlutaric aciduria I details
Cerebrospinal Fluid (CSF)Detected and Quantified4450 uMNot AvailableNot Specified
Glutaryl-CoA dehydrogenase deficiency (GDHD)
details
Cerebrospinal Fluid (CSF)Detected and Quantified4450 uMChildren (1-13 years old)Not SpecifiedGlutaric acid excretion above 100 mmol/mol creatinine details
Cerebrospinal Fluid (CSF)Detected and Quantified2.2 uMNewborn (0-30 days old)MaleGlutaric aciduria I details
UrineDetected and Quantified3.68 umol/mmol creatinineAdolescent (13-18 years old)FemaleGlutaric aciduria I details
UrineDetected and Quantified590 umol/mmol creatinineNewborn (0-30 days old)MaleGlutaric aciduria I details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease References
Glutaric aciduria I
  1. Poge AP, Autschbach F, Korall H, Trefz FK, Mayatepek E: Early clinical manifestation of glutaric aciduria type I and nephrotic syndrome during the first months of life. Acta Paediatr. 1997 Oct;86(10):1144-7. [PubMed:9350903 ]
  2. Fraidakis MJ, Liadinioti C, Stefanis L, Dinopoulos A, Pons R, Papathanassiou M, Garcia-Villoria J, Ribes A: Rare Late-Onset Presentation of Glutaric Aciduria Type I in a 16-Year-Old Woman with a Novel GCDH Mutation. JIMD Rep. 2015;18:85-92. doi: 10.1007/8904_2014_353. Epub 2014 Sep 26. [PubMed:25256449 ]
  3. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Glutaryl-CoA dehydrogenase deficiency (GDHD)
  1. Baric I, Wagner L, Feyh P, Liesert M, Buckel W, Hoffmann GF: Sensitivity and specificity of free and total glutaric acid and 3-hydroxyglutaric acid measurements by stable-isotope dilution assays for the diagnosis of glutaric aciduria type I. J Inherit Metab Dis. 1999 Dec;22(8):867-81. [PubMed:10604139 ]
Associated OMIM IDsNone
DrugBank IDDB04594
Phenol Explorer Compound IDNot Available
FooDB IDFDB022040
KNApSAcK IDNot Available
Chemspider ID158277
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAlpha-Hydroxyglutaric acid
METLIN ID5417
PubChem Compound181976
PDB IDNot Available
ChEBI ID39980
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000160
Good Scents IDNot Available
References
Synthesis ReferenceArnaud, Nathalie; Picard, Claude; Cazaux, Louis; Tisnes, Pierre. Synthesis of macrocyclic polyhydroxy tetralactams derived from L-tartaric acid and b-hydroxyglutaric acid. Tetrahedron (1997), 53(40), 13757-13768.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Baric I, Wagner L, Feyh P, Liesert M, Buckel W, Hoffmann GF: Sensitivity and specificity of free and total glutaric acid and 3-hydroxyglutaric acid measurements by stable-isotope dilution assays for the diagnosis of glutaric aciduria type I. J Inherit Metab Dis. 1999 Dec;22(8):867-81. [PubMed:10604139 ]
  2. Kolker S, Hoffmann GF, Schor DS, Feyh P, Wagner L, Jeffrey I, Pourfarzam M, Okun JG, Zschocke J, Baric I, Bain MD, Jakobs C, Chalmers RA: Glutaryl-CoA dehydrogenase deficiency: region-specific analysis of organic acids and acylcarnitines in post mortem brain predicts vulnerability of the putamen. Neuropediatrics. 2003 Jun;34(5):253-60. [PubMed:14598231 ]
  3. Wajner M, Kolker S, Souza DO, Hoffmann GF, de Mello CF: Modulation of glutamatergic and GABAergic neurotransmission in glutaryl-CoA dehydrogenase deficiency. J Inherit Metab Dis. 2004;27(6):825-8. [PubMed:15505388 ]
  4. Nyhan WL, Zschocke J, Hoffmann G, Stein DE, Bao L, Goodman S: Glutaryl-CoA dehydrogenase deficiency presenting as 3-hydroxyglutaric aciduria. Mol Genet Metab. 1999 Mar;66(3):199-204. [PubMed:10066389 ]
  5. Molven A, Matre GE, Duran M, Wanders RJ, Rishaug U, Njolstad PR, Jellum E, Sovik O: Familial hyperinsulinemic hypoglycemia caused by a defect in the SCHAD enzyme of mitochondrial fatty acid oxidation. Diabetes. 2004 Jan;53(1):221-7. [PubMed:14693719 ]
  6. Haworth JC, Booth FA, Chudley AE, deGroot GW, Dilling LA, Goodman SI, Greenberg CR, Mallory CJ, McClarty BM, Seshia SS, et al.: Phenotypic variability in glutaric aciduria type I: Report of fourteen cases in five Canadian Indian kindreds. J Pediatr. 1991 Jan;118(1):52-8. [PubMed:1986098 ]
  7. Sauer SW, Okun JG, Fricker G, Mahringer A, Muller I, Crnic LR, Muhlhausen C, Hoffmann GF, Horster F, Goodman SI, Harding CO, Koeller DM, Kolker S: Intracerebral accumulation of glutaric and 3-hydroxyglutaric acids secondary to limited flux across the blood-brain barrier constitute a biochemical risk factor for neurodegeneration in glutaryl-CoA dehydrogenase deficiency. J Neurochem. 2006 May;97(3):899-910. Epub 2006 Mar 29. [PubMed:16573641 ]