MiMeDB: Showing metabocard for (4R)-4-hydroxy-2-oxoglutarate (MMDBc0054952)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:38:30 UTC

Update Date

2022-08-12 20:09:10 UTC

Metabolite ID

MMDBc0054952

Metabolite Identification

Common Name

(4R)-4-hydroxy-2-oxoglutarate

Description

D-4-hydroxy-2-ketoglutarate, also known as (R)-2-hydroxy-4-oxopentanedioate, belongs to the class of organic compounds known as gamma-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom. Based on a literature review very few articles have been published on D-4-hydroxy-2-ketoglutarate.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4    6   12                                             
CONECT    3    1    5    7                                                  
CONECT    4    2    8    9                                                  
CONECT    5    3   10   11                                                  
CONECT    6    2                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
(4R)-4-Hydroxy-2-oxoglutarate	ChEBI
(R)-2-Hydroxy-4-oxopentanedioate	ChEBI
D-4-Hydroxy-2-oxoglutarate dianion	ChEBI
(4R)-4-Hydroxy-2-oxoglutaric acid	Generator
(R)-2-Hydroxy-4-oxopentanedioic acid	Generator
D-4-Hydroxy-2-oxoglutaric acid dianion	Generator
D-4-Hydroxy-2-ketoglutaric acid	Generator

Molecular Formula

C₅H₄O₆

Average Mass

160.082

Monoisotopic Mass

160.001885009

IUPAC Name

(2R)-2-hydroxy-4-oxopentanedioate

Traditional Name

D-4-hydroxy-2-oxoglutarate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CC(=O)C([O-])=O)C([O-])=O

InChI Identifier

InChI=1S/C5H6O6/c6-2(4(8)9)1-3(7)5(10)11/h2,6H,1H2,(H,8,9)(H,10,11)/p-2/t2-/m1/s1

InChI Key

WXSKVKPSMAHCSG-UWTATZPHSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Gamma-keto acids and derivatives

Direct Parent

Gamma-keto acids and derivatives

Alternative Parents

Substituents

Gamma-keto acid
Short-chain keto acid
Dicarboxylic acid or derivatives
Beta-hydroxy ketone
Alpha-keto acid
Secondary alcohol
Ketone
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Alcohol
Organooxygen compound
Organic oxygen compound
Carbonyl group
Organic oxide
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

4-hydroxy-2-oxoglutarate(2-) (CHEBI:62213 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-0.82	ChemAxon
pKa (Strongest Acidic)	2.45	ChemAxon
pKa (Strongest Basic)	-3.9	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	117.56 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	51.9 m³·mol⁻¹	ChemAxon
Polarizability	12.08 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

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0015006	(4R)-4-hydroxy-2-oxoglutarate	glyoxylate	KHG/KDPG aldolase	Aldol addition (or reverse)	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites
Bacteria	Firmicutes	1	Human feces
Bacteria	Proteobacteria	8	Human ; Human feces
Bacteria	Spirochaetes	1	Human
Eukaryota/Fungi	Ascomycota	2

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

52921639

PDB ID

Not Available

ChEBI ID

62213

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (4R)-4-hydroxy-2-oxoglutarate (MMDBc0054952)

MOL for #<Metabolite:0x00007f5abd627568>

3D MOL for #<Metabolite:0x00007f5abd627568>

3D SDF for #<Metabolite:0x00007f5abd627568>

3D-SDF for #<Metabolite:0x00007f5abd627568>

PDB for #<Metabolite:0x00007f5abd627568>

3D PDB for #<Metabolite:0x00007f5abd627568>

SMILES for #<Metabolite:0x00007f5abd627568>

INCHI for #<Metabolite:0x00007f5abd627568>

Structure for #<Metabolite:0x00007f5abd627568>

3D Structure for #<Metabolite:0x00007f5abd627568>