Showing Compound Card for D-2-Hydroxyglutaric acid (CDB004849)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraProtein targetPathwaysConcentrationsLinksReferencesenzymes (3) Show 4 proteinsXML
Record Information
Version1.0
Created at2020-04-17 18:43:08 UTC
Updated at2020-12-07 19:11:06 UTC
CannabisDB IDCDB004849
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NameD-2-Hydroxyglutaric acid
DescriptionD-2-Hydroxyglutaric acid, also known as (R)-hydroxyglutarate or (R)-2-hydroxy-pentanedioate, 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. D-2-Hydroxyglutaric acid is an extremely weak basic (essentially neutral) compound (based on its pKa). D-2-Hydroxyglutaric acid exists in all living organisms, ranging from bacteria to humans. D-2-hydroxyglutaric acid can be biosynthesized from oxoglutaric acid through the action of the enzyme D-2-hydroxyglutarate dehydrogenase, mitochondrial. In humans, D-2-hydroxyglutaric acid is involved in the metabolic disorder called the oncogenic action of d-2-hydroxyglutarate in hydroxyglutaric aciduria. Outside of the human body, D-2-Hydroxyglutaric acid has been detected, but not quantified in, milk (cow). This could make D-2-hydroxyglutaric acid a potential biomarker for the consumption of these foods. D-2-Hydroxyglutaric acid is a potentially toxic compound. D-2-Hydroxyglutaric acid, with regard to humans, has been found to be associated with several diseases such as d, l-2-hydroxyglutaric aciduria and spondyloenchondrodysplasia; D-2-hydroxyglutaric acid has also been linked to the inborn metabolic disorder d-2-hydroxyglutaric aciduria. The (R)-enantiomer of 2-hydroxyglutaric acid. D-2-Hydroxyglutaric acid is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
(R)-2-HydroxyglutarateChEBI
(R)-HydroxyglutarateChEBI
(R)-2-Hydroxyglutaric acidGenerator
(R)-Hydroxyglutaric acidGenerator
D-2-HydroxyglutarateGenerator
(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-a-HydroxyglutarateHMDB
D-a-Hydroxyglutaric acidHMDB
delta-2-HydroxyglutarateHMDB
delta-2-Hydroxyglutaric acidHMDB
delta-alpha-HydroxyglutarateHMDB
delta-alpha-Hydroxyglutaric acidHMDB
2-HydroxyglutarateHMDB
alpha-Hydroxyglutarate, (D)-isomerHMDB
alpha-Hydroxyglutarate, (DL)-isomerHMDB
2-Hydroxyglutaric acidHMDB
alpha-HydroxyglutarateHMDB
alpha-Hydroxyglutarate, (L)-isomerHMDB
alpha-Hydroxyglutarate, disodium saltHMDB
Chemical FormulaC5H8O5
Average Molecular Weight148.11
Monoisotopic Molecular Weight148.0372
IUPAC Name(2R)-2-hydroxypentanedioic acid
Traditional NameD-2-hydroxyglutaric acid
CAS Registry Number13095-47-1
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-/m1/s1
InChI KeyHWXBTNAVRSUOJR-GSVOUGTGSA-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

Source:

Biological location:

Role

Indirect biological role:

Biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
logPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSD-2-Hydroxyglutaric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0zgl-9300000000-805667744aba36281cecSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-00gv-8191000000-f6fdffd87ffe1acf65b4Spectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSD-2-Hydroxyglutaric acid, TBDMS_3_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001j-1900000000-dbf80fc2b86ec60d623e2016-06-03View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0m5r-9600000000-d1bc7ce2206164b5bc2c2016-06-03View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9000000000-df3e77cb42d6f7647a642016-06-03View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-1900000000-095c1140772d4cdd149b2016-08-03View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0zfr-7900000000-ce158ac5b56eff8677352016-08-03View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9000000000-e30760384709aa9789862016-08-03View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0fbi-3900000000-f88fcf3ac0dd06636b162021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0k9i-9400000000-31bf8d3bb7203e7bf2002021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4u-9000000000-c0ac45c4d66178ac20cf2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0w39-4900000000-1385b471f7cdf14ca14d2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-052r-9500000000-17ece6956644d4cf20692021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4r-9000000000-dbb4195080bddb5f62102021-09-22View Spectrum
NMRNot Available
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
D-3-phosphoglycerate dehydrogenasePHGDH1p12O43175 details
D-2-hydroxyglutarate dehydrogenase, mitochondrialD2HGDH2q37.3Q8N465 details
Hydroxyacid-oxoacid transhydrogenase, mitochondrialADHFE18q13.1Q8IWW8 details
TransportersNot Available
Metal Bindings
Protein NameGene NameLocusUniprot IDDetails
Hydroxyacid-oxoacid transhydrogenase, mitochondrialADHFE18q13.1Q8IWW8 details
ReceptorsNot Available
Transcriptional FactorsNot Available
Concentrations Data
Not Available
HMDB IDHMDB0000606
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022139
KNApSAcK IDNot Available
Chemspider ID388508
KEGG Compound IDC01087
BioCyc IDR-2-HYDROXYGLUTARATE
BiGG IDNot Available
Wikipedia LinkAlpha-Hydroxyglutaric acid
METLIN ID5581
PubChem Compound439391
PDB IDNot Available
ChEBI ID32796
References
General ReferencesNot Available

Enzymes

Enzyme Details
1. D-3-phosphoglycerate dehydrogenase
General function:
Involved in phosphoglycerate dehydrogenase activity
Specific function:
Not Available
Gene Name:
PHGDH
Uniprot ID:
O43175
Molecular weight:
56650.03
Enzyme Details
2. D-2-hydroxyglutarate dehydrogenase, mitochondrial
General function:
Involved in catalytic activity
Specific function:
Catalyzes the oxidation of D-2-hydroxyglutarate to alpha-ketoglutarate.
Gene Name:
D2HGDH
Uniprot ID:
Q8N465
Molecular weight:
56415.58
Enzyme Details
3. Hydroxyacid-oxoacid transhydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the cofactor-independent reversible oxidation of gamma-hydroxybutyrate (GHB) to succinic semialdehyde (SSA) coupled to reduction of 2-ketoglutarate (2-KG) to D-2-hydroxyglutarate (D-2-HG). D,L-3-hydroxyisobutyrate and L-3-hydroxybutyrate (L-3-OHB) are also substrates for HOT with 10-fold lower activities.
Gene Name:
ADHFE1
Uniprot ID:
Q8IWW8
Molecular weight:
50307.42