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

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Record Information

Version

1.0

Created at

2020-04-17 18:43:08 UTC

Updated at

2020-12-07 19:11:06 UTC

CannabisDB ID

CDB004849

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

D-2-Hydroxyglutaric acid

Description

D-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

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms

Value	Source
(R)-2-Hydroxyglutarate	ChEBI
(R)-Hydroxyglutarate	ChEBI
(R)-2-Hydroxyglutaric acid	Generator
(R)-Hydroxyglutaric acid	Generator
D-2-Hydroxyglutarate	Generator
(R)-2-Hydroxy-pentanedioate	HMDB
(R)-2-Hydroxy-pentanedioic acid	HMDB
(R)-a-Hydroxyglutarate	HMDB
(R)-a-Hydroxyglutaric acid	HMDB
(R)-alpha-Hydroxyglutarate	HMDB
(R)-alpha-Hydroxyglutaric acid	HMDB
2-Hydroxy-D-glutarate	HMDB
2-Hydroxy-D-glutaric acid	HMDB
2-Hydroxy-delta-glutarate	HMDB
2-Hydroxy-delta-glutaric acid	HMDB
D-a-Hydroxyglutarate	HMDB
D-a-Hydroxyglutaric acid	HMDB
delta-2-Hydroxyglutarate	HMDB
delta-2-Hydroxyglutaric acid	HMDB
delta-alpha-Hydroxyglutarate	HMDB
delta-alpha-Hydroxyglutaric acid	HMDB
2-Hydroxyglutarate	HMDB
alpha-Hydroxyglutarate, (D)-isomer	HMDB
alpha-Hydroxyglutarate, (DL)-isomer	HMDB
2-Hydroxyglutaric acid	HMDB
alpha-Hydroxyglutarate	HMDB
alpha-Hydroxyglutarate, (L)-isomer	HMDB
alpha-Hydroxyglutarate, disodium salt	HMDB

Chemical Formula

C₅H₈O₅

Average Molecular Weight

148.11

Monoisotopic Molecular Weight

148.0372

IUPAC Name

(2R)-2-hydroxypentanedioic acid

Traditional Name

D-2-hydroxyglutaric acid

CAS Registry Number

13095-47-1

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 Key

HWXBTNAVRSUOJR-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.

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-hydroxyglutaric acid (CHEBI:32796 )

Ontology

Endogenous

Biological:

Microbe

Biological location:

Tissue and substructures:

Placenta

Organ and components:

Brain

Subcellular:

Biofluid and excreta:

Role

Indirect biological role:

Biological role:

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	> 300 °C	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	D-2-Hydroxyglutaric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0zgl-9300000000-805667744aba36281cec	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-00gv-8191000000-f6fdffd87ffe1acf65b4	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	D-2-Hydroxyglutaric acid, TBDMS_3_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001j-1900000000-dbf80fc2b86ec60d623e	2016-06-03	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0m5r-9600000000-d1bc7ce2206164b5bc2c	2016-06-03	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-df3e77cb42d6f7647a64	2016-06-03	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1900000000-095c1140772d4cdd149b	2016-08-03	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zfr-7900000000-ce158ac5b56eff867735	2016-08-03	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-e30760384709aa978986	2016-08-03	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0fbi-3900000000-f88fcf3ac0dd06636b16	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0k9i-9400000000-31bf8d3bb7203e7bf200	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4u-9000000000-c0ac45c4d66178ac20cf	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0w39-4900000000-1385b471f7cdf14ca14d	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-052r-9500000000-17ece6956644d4cf2069	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4r-9000000000-dbb4195080bddb5f6210	2021-09-22	View Spectrum

NMR

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
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
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

HMDB0000606

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022139

KNApSAcK ID

Not Available

Chemspider ID

388508

KEGG Compound ID

C01087

BioCyc ID

R-2-HYDROXYGLUTARATE

BiGG ID

Not Available

Wikipedia Link

Alpha-Hydroxyglutaric acid

METLIN ID

5581

PubChem Compound

439391

PDB ID

Not Available

ChEBI ID

32796

References

General References

Not 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

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

Structure for CDB004849 (D-2-Hydroxyglutaric acid)

Enzymes