Milk Composition Database: Showing metabocard for D-2-Hydroxyglutaric acid (BMDB0000606)

Identification Taxonomy Physical properties Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:33:28 UTC

Update Date

2020-05-11 20:37:16 UTC

MCDB ID

BMDB0000606

Secondary Accession Numbers

BMDB00606

Metabolite 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 exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. D-2-Hydroxyglutaric acid exists in all living organisms, ranging from bacteria to humans. D-2-Hydroxyglutaric acid is a potentially toxic compound. D-2-Hydroxyglutaric acid has been found to be associated with several diseases known as spondyloenchondrodysplasia and d, l-2-hydroxyglutaric aciduria; also d-2-hydroxyglutaric acid has been linked to the inborn metabolic disorders including d-2-hydroxyglutaric aciduria.

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

148.114

Monoisotopic Molecular Weight

148.037173366

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 )

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	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0zgl-9300000000-805667744aba36281cec	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00gv-8191000000-f6fdffd87ffe1acf65b4	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001j-1900000000-dbf80fc2b86ec60d623e	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0m5r-9600000000-d1bc7ce2206164b5bc2c	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-df3e77cb42d6f7647a64	2016-06-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1900000000-095c1140772d4cdd149b	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zfr-7900000000-ce158ac5b56eff867735	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-e30760384709aa978986	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0fbi-3900000000-f88fcf3ac0dd06636b16	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0k9i-9400000000-31bf8d3bb7203e7bf200	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4u-9000000000-c0ac45c4d66178ac20cf	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0w39-4900000000-1385b471f7cdf14ca14d	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-052r-9500000000-17ece6956644d4cf2069	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4r-9000000000-dbb4195080bddb5f6210	2021-09-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	2021-09-16	View Spectrum

Concentrations

Status	Value		Reference	Details
Detected but not Quantified	Not Applicable		PMID: 23438684	details

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

Synthesis Reference

Kobayashi, Hidehiko; Yamaguchi, Koretaka; Yamashita, Takeshi. a-Hydroxyglutaric acid from glutamic acid. Jpn. Tokkyo Koho (1968), 3 pp.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]

Showing metabocard for D-2-Hydroxyglutaric acid (BMDB0000606)

Structure for BMDB0000606 (D-2-Hydroxyglutaric acid)