ECMDB: D-2-Hydroxyglutaric acid (ECMDB00606) (M2MDB000155)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (1)XML

Proteins (121)

Record Information

Version

2.0

Creation Date

2012-05-31 10:27:42 -0600

Update Date

2015-09-13 12:56:08 -0600

Secondary Accession Numbers

ECMDB00606

Identification

Name:

D-2-Hydroxyglutaric acid

Description

D-2-Hydroxyglutaric acid is a member of the chemical class known as Short-chain Hydroxy Acids and Derivatives. These are hydroxy acids with an alkyl chain the contains less than 6 carbon atoms.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

(R)-2-hydroxy-Pentanedioate
(R)-2-hydroxy-Pentanedioic acid
(R)-2-Hydroxyglutarate
(R)-2-Hydroxyglutaric acid
(R)-a-Hydroxyglutarate
(R)-a-Hydroxyglutaric acid
(R)-alpha-Hydroxyglutarate
(R)-alpha-Hydroxyglutaric acid
(R)-α-Hydroxyglutarate
(R)-α-Hydroxyglutaric acid
2-Hydroxy-D-Glutarate
2-Hydroxy-D-Glutaric acid
D-2-Hydroxyglutarate
D-2-Hydroxyglutaric acid
D-a-Hydroxyglutarate
D-a-Hydroxyglutaric acid
D-alpha-Hydroxyglutarate
D-alpha-Hydroxyglutaric acid
D-α-Hydroxyglutarate
D-α-Hydroxyglutaric acid

Chemical Formula:

C₅H₈O₅

Weight:

Average: 148.114
Monoisotopic: 148.037173366

InChI Key:

HWXBTNAVRSUOJR-UHFFFAOYSA-N

InChI:

InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)

CAS number:

13095-47-1

IUPAC Name:

2-hydroxypentanedioic acid

Traditional IUPAC Name:

2-hydroxyglutaric acid

SMILES:

OC(CCC(O)=O)C(O)=O

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 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

>300 °C

Experimental Properties:

Property	Value	Source
LogP:	-0.979	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	157 g/L	ALOGPS
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	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

D-2-Hydroxyglutaric acid + NAD > Oxoglutaric acid + NADH
3-Phospho-D-glycerate + NAD + D-2-Hydroxyglutaric acid <> Phosphohydroxypyruvic acid + NADH + Hydrogen ion + alpha-Ketoglutarate

SMPDB Pathways:

Not Available

KEGG Pathways:

Glycine, serine and threonine metabolism ec00260
Metabolic pathways eco01100
Methane metabolism ec00680
Microbial metabolism in diverse environments ec01120

EcoCyc Pathways:

Not Available

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0uel-9300000000-fbe125fbbc3b5bc0783b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00gv-8191000000-f6fdffd87ffe1acf65b4	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 0V, negative	splash10-0002-0900000000-09163ea46c418972472c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-0002-0900000000-d04b995445fdf4b9a53d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-0002-0900000000-b0a25d5d220611188e25	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-0002-0900000000-fffbc099f0f67f0511f3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-0002-0900000000-09f10084fba5e519de0a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-002b-0900000000-dff435b3dcd956320479	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, negative	splash10-004j-0900000000-bda2b170e24c7a9e5c35	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, negative	splash10-004i-0900000000-73ae87a8fb9bc7ee539d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-0fb9-1900000000-b1dc0a848bf8324490a7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, negative	splash10-0ug0-3900000000-07793b211b4728e17669	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 6V, negative	splash10-0udr-6900000000-f034f6e5155f6da3db5a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 10V, negative	splash10-004i-0900000000-80c3e765d7538561ccbf	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 10V, negative	splash10-000i-9300000000-7ffbc20d629772e358cc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-004i-0900000000-982cc580a7d58e352fcb	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, negative	splash10-004i-1900000000-5920ffef63672e32cc73	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-004i-2900000000-0945bfdbb47d1208ca55	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 2V, negative	splash10-004r-3900000000-8a092cb937763eb031bb	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, negative	splash10-004r-6900000000-41fa2c2ee20825e5b11d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-002r-9800000000-6677f366953c5f35a17b	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, negative	splash10-000i-9500000000-0ca597332561395d2cc3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, negative	splash10-000i-9400000000-510a9566cf27424fa58c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 10V, negative	splash10-0udr-4900000000-cf48fcc4c8561ba5a0e0	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, positive	splash10-00di-9000000000-36768b96f759cfee016d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 10V, positive	splash10-0udi-0900000000-47e5cb48d7b683b18747	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 1V, positive	splash10-03dj-1790000000-8eb0579a5917747d340e	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CHEBI ID	32796
HMDB ID	HMDB00606
Pubchem Compound ID	43
Kegg ID	C02630
ChemSpider ID	42
Wikipedia ID	Alpha-Hydroxyglutaric_acid
BioCyc ID	Not Available

Enzymes

Protein Details

1. D-3-phosphoglycerate dehydrogenase

General function:: Involved in amino acid binding
Specific function:: 3-phospho-D-glycerate + NAD(+) = 3- phosphonooxypyruvate + NADH
Gene Name:: serA
Uniprot ID:: P0A9T0
Molecular weight:: 44175

Reactions

3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH.
2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH.

D-2-Hydroxyglutaric acid (ECMDB00606) (M2MDB000155)

Structure for #<Compound:0xa7327dbc>

Enzymes

Reactions