Cannabis Compound Database: Showing Compound Card for 2-Hydroxyglutarate (CDB005137)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (4) Show 5 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 19:13:03 UTC

Updated at

2020-12-07 19:11:39 UTC

CannabisDB ID

CDB005137

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

2-Hydroxyglutarate

Description

2-Hydroxyglutarate 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. 2-Hydroxyglutarate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 2-Hydroxyglutarate exists in all living species, ranging from bacteria to humans. 2-hydroxyglutarate can be biosynthesized from oxoglutaric acid through the action of the enzyme L-2-hydroxyglutarate dehydrogenase, mitochondrial. In humans, 2-hydroxyglutarate is involved in the metabolic disorder called the oncogenic action of d-2-hydroxyglutarate in hydroxyglutaric aciduria. In cancer it is either produced by overexpression of phosphoglycerate dehydrogenase (PHGDH) or is produced in excess by gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). A deficiency in either of these two enzymes can lead to a disease known as 2-hydroxyglutaric aciduria. 2-Hydroxyglutarate exists in 2 isomers: L-2-hydroxyglutarate acid and D-2-hydroxyglutarate. D-2-hydroxyglutaric aciduria (caused by loss of D2HGDH or gain of function of IDH) is rare, with symptoms including cancer, macrocephaly, cardiomyopathy, mental retardation, hypotonia, and cortical blindness. 2-Hydroxyglutarate is a potentially toxic compound. 2-Hydroxyglutarate, with regard to humans, has been found to be associated with several diseases such as deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures syndrome, d, l-2-hydroxyglutaric aciduria, supragingival plaque, and colorectal cancer; 2-hydroxyglutarate has also been linked to the inborn metabolic disorder l-2-hydroxyglutaric aciduria. 2-Hydroxyglutarate has also been found to be a metabolite in Aspergillus (PMID: 6057807 ). 2-hydroxyglutarate is also the product of gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). In humans it is part of butanoate metabolic pathway and can be produced by phosphoglycerate dehydrogenase (PHGDH). Humans have to variants of this enzyme: 2-Hydroxyglutarate dehydrogenase (D2HGDH) and L-2-hydroxyglutarate dehydrogenase (L2HGDH). 2-Hydroxyglutarate is expected to be in Cannabis as all living plants are known to produce and metabolize it.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
alpha-Hydroxyglutaric acid	ChEBI
alpha-Hydroxyglutarate	Kegg
a-Hydroxyglutarate	Generator
a-Hydroxyglutaric acid	Generator
Α-hydroxyglutarate	Generator
Α-hydroxyglutaric acid	Generator
2-Hydroxyglutaric acid	Generator
D-2-Hydroxyglutarate	HMDB
alpha-Hydroxyglutarate, (D)-isomer	HMDB
alpha-Hydroxyglutarate, (DL)-isomer	HMDB
alpha-Hydroxyglutarate, (L)-isomer	HMDB
alpha-Hydroxyglutarate, disodium salt	HMDB
(±)-2-hydroxyglutaric acid	HMDB
2,3-Dideoxypentaric acid	HMDB
2-Hydroxypentanedioic acid	HMDB
DL-2-Hydroxyglutaric acid	HMDB
2-Hydroxyglutarate	Generator

Chemical Formula

C₅H₈O₅

Average Molecular Weight

148.11

Monoisotopic Molecular Weight

148.0372

IUPAC Name

2-hydroxypentanedioic acid

Traditional Name

2-hydroxyglutaric acid

CAS Registry Number

2889-31-8

SMILES

OC(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)

InChI Key

HWXBTNAVRSUOJR-UHFFFAOYSA-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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Short-chain hydroxy acids and derivatives

Direct Parent

Short-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 Framework

Aliphatic acyclic compounds

External Descriptors

2-hydroxydicarboxylic acid (CHEBI:17084 )

Ontology

Physiological effect

Health effect:

Observation:

Supragingival Plaque

Health condition:

Disposition

Source:

Endogenous

Biological:

Microbe

Fungi:

Aspergillus:

Aspergillus glaucus

Biological location:

Organ and components:

Brain

Subcellular:

Biofluid and excreta:

Role

Biological role:

Waste product

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
logP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1	ALOGPS
logP	-0.82	ChemAxon
logS	0.03	ALOGPS
pKa (Strongest Acidic)	3.28	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	29.63 m³·mol⁻¹	ChemAxon
Polarizability	12.97 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	2-Hydroxyglutarate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0uel-9300000000-fbe125fbbc3b5bc0783b	Spectrum
Predicted GC-MS	2-Hydroxyglutarate, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-00gv-8191000000-f6fdffd87ffe1acf65b4	Spectrum
Predicted GC-MS	2-Hydroxyglutarate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - Orbitrap 0V, negative	splash10-0002-0900000000-09163ea46c418972472c	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-0002-0900000000-d04b995445fdf4b9a53d	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-0002-0900000000-b0a25d5d220611188e25	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-0002-0900000000-fffbc099f0f67f0511f3	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-0002-0900000000-09f10084fba5e519de0a	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-002b-0900000000-dff435b3dcd956320479	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, negative	splash10-004j-0900000000-bda2b170e24c7a9e5c35	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, negative	splash10-004i-0900000000-73ae87a8fb9bc7ee539d	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-0fb9-1900000000-b1dc0a848bf8324490a7	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, negative	splash10-0ug0-3900000000-07793b211b4728e17669	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 6V, negative	splash10-0udr-6900000000-f034f6e5155f6da3db5a	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 10V, negative	splash10-004i-0900000000-80c3e765d7538561ccbf	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 10V, negative	splash10-000i-9300000000-7ffbc20d629772e358cc	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-004i-0900000000-982cc580a7d58e352fcb	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-004i-1900000000-5920ffef63672e32cc73	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-004i-2900000000-0945bfdbb47d1208ca55	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-004r-3900000000-8a092cb937763eb031bb	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, negative	splash10-004r-6900000000-41fa2c2ee20825e5b11d	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-002r-9800000000-6677f366953c5f35a17b	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-000i-9500000000-0ca597332561395d2cc3	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, negative	splash10-000i-9400000000-510a9566cf27424fa58c	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 10V, negative	splash10-0udr-4900000000-cf48fcc4c8561ba5a0e0	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, positive	splash10-00di-9000000000-36768b96f759cfee016d	2020-07-21	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 10V, positive	splash10-0udi-0900000000-47e5cb48d7b683b18747	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, positive	splash10-03dj-1790000000-8eb0579a5917747d340e	2020-07-22	View Spectrum

NMR

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
The oncogenic action of 2-hydroxyglutarate		Not Available
The Oncogenic Action of Succinate		Not Available
The Oncogenic Action of Fumarate		Not Available
The oncogenic action of D-2-hydroxyglutarate in Hydroxygluaricaciduria		Not Available
The oncogenic action of L-2-hydroxyglutarate in Hydroxygluaricaciduria		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
D-3-phosphoglycerate dehydrogenase	PHGDH	1p12	O43175	details
D-2-hydroxyglutarate dehydrogenase, mitochondrial	D2HGDH	2q37.3	Q8N465	details
L-2-hydroxyglutarate dehydrogenase, mitochondrial	L2HGDH	14q21.3	Q9H9P8	details
Hydroxyacid-oxoacid transhydrogenase, mitochondrial	ADHFE1	8q13.1	Q8IWW8	details

Transporters

Not Available

Metal Bindings

Protein Name	Gene Name	Locus	Uniprot ID	Details
Hydroxyacid-oxoacid transhydrogenase, mitochondrial	ADHFE1	8q13.1	Q8IWW8	details

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0059655

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

C02630

BioCyc ID

2-HYDROXYGLUTARIC_ACID

BiGG ID

Not Available

Wikipedia Link

Alpha-Hydroxyglutaric_acid

METLIN ID

Not Available

PubChem Compound

PDB ID

Not Available

ChEBI ID

17084

References

General References

Bleiweis AS, Reeves HC, Ajl SJ: Formation of alpha-hydroxyglutaric acid by Aspergillus glaucus. J Bacteriol. 1967 Nov;94(5):1560-4. [PubMed:6057807 ]

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. L-2-hydroxyglutarate dehydrogenase, mitochondrial

General function:: Involved in 2-hydroxyglutarate dehydrogenase activity
Specific function:: Not Available
Gene Name:: L2HGDH
Uniprot ID:: Q9H9P8
Molecular weight:: 50315.58

Enzyme Details

4. 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

Showing Compound Card for 2-Hydroxyglutarate (CDB005137)

Structure for CDB005137 (2-Hydroxyglutarate)

Enzymes