MiMeDB: Showing metabocard for 2-Dehydro-D-gluconate (MMDBc0029765)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:40:41 UTC

Update Date

2022-08-31 17:16:47 UTC

Metabolite ID

MMDBc0029765

Metabolite Identification

Common Name

2-Dehydro-D-gluconate

Description

2-Keto-L-gluconate is a derivative of gluconic acid, which occurs naturally in fruit, honey and wine and is used as a food additive, an acidity regulator. It is also used in cleaning products where it helps cleaning up mineral deposits. It is a strong chelating agent, especially in alkaline solution. It chelates the anions of calcium, iron, aluminium, copper, and other heavy metals. E. coli contains ketogluconate reductase genes, so it is likely that pathways exist for the metabolism of ketogluconate

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      30.343 -25.371   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      30.343 -26.911   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      29.009 -27.681   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.676 -26.911   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      26.342 -27.681   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.342 -29.221   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      29.009 -24.601   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      31.677 -27.681   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      29.009 -29.221   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      27.676 -25.371   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      25.008 -26.911   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      25.008 -29.991   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      27.676 -29.991   0.000  0.00  0.00           O+0
CONECT    1    7    2                                                       
CONECT    2    1    8    3                                                  
CONECT    3    2    9    4                                                  
CONECT    4    3   10    5                                                  
CONECT    5    4   11    6                                                  
CONECT    6    5   12   13                                                  
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
2-Keto-L-gluconic acid	Generator
2-Dehydro-D-gluconate	HMDB
2-Dehydro-L-idonate	HMDB
2-Keto-D-gluconate	HMDB
2-Keto-L-gulonate	HMDB
2-Ketoidonate	HMDB
2-Oxogluconic acid	HMDB
L-Ketoidonate	HMDB
L-Ketoidonic acid	HMDB
L-Sorbosonate	HMDB
L-Sorbosonic acid	HMDB
Provitamin C	HMDB
Provitamin C, monosodium salt	HMDB
2-Keto-L-gulonic acid	HMDB
Provitamin C, (L-xylo)-isomer	HMDB
2-Dehydro-L-gluconate	Generator

Molecular Formula

C₆H₁₀O₇

Average Mass

194.1394

Monoisotopic Mass

194.042652674

IUPAC Name

3,4,5,6-tetrahydroxy-2-oxohexanoic acid

Traditional Name

2-keto-D-gluconic acid

CAS Registry Number

Not Available

SMILES

OCC(O)C(O)C(O)C(=O)C(O)=O

InChI Identifier

InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-4,7-10H,1H2,(H,12,13)

InChI Key

VBUYCZFBVCCYFD-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Hexose monosaccharide
Medium-chain keto acid
Beta-hydroxy acid
Sugar acid
Acyloin
Alpha-keto acid
Beta-hydroxy ketone
Hydroxy acid
Keto acid
Monosaccharide
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Polyol
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	101 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-2.5	ChemAxon
logS	-0.28	ALOGPS
pKa (Strongest Acidic)	2.67	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	135.29 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	37.65 m³·mol⁻¹	ChemAxon
Polarizability	16.3 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

Feces

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019089	2,5-Diketo-D-gluconate	2-Dehydro-D-gluconate	2,5-diketo-D-gluconic acid reductase B	Reduction	PathBank	31602464
MMDBr0019090	2-Dehydro-D-gluconate	L-Idonic acid	Glyoxylate/hydroxypyruvate reductase B	Reduction	PathBank	31602464
MMDBr0019100	2-Dehydro-D-gluconate	Gluconic acid	2,3-diketo-L-gulonate reductase	Reduction	PathBank	31602464
MMDBr0024432	D-gluconic acid	2-Dehydro-D-gluconate	Gluconate 2-dehydrogenase subunit 3	Dehydrogenation	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	Microbial Links
Bacteria	Proteobacteria	2	Human feces; Human ; Human feces; pleural fluid plaque; bal; Human stool; Human sputum	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	54	Human feces; Human ; Human feces; pleural fluid plaque; bal; Human stool; Human sputum	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	17	Human ; Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	1
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Feces	Detected but not Quantified						Infant (0-1 year old)	Both	Normal	HMDB	22411374

External Links

HMDB ID

HMDB0011732

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028412

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

C03342

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

PDB ID

Not Available

ChEBI ID

88378

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 2-Dehydro-D-gluconate (MMDBc0029765)

MOL for #<Metabolite:0x00005645c9de4b48>

3D MOL for #<Metabolite:0x00005645c9de4b48>

3D SDF for #<Metabolite:0x00005645c9de4b48>

3D-SDF for #<Metabolite:0x00005645c9de4b48>

PDB for #<Metabolite:0x00005645c9de4b48>

3D PDB for #<Metabolite:0x00005645c9de4b48>

SMILES for #<Metabolite:0x00005645c9de4b48>

INCHI for #<Metabolite:0x00005645c9de4b48>

Structure for #<Metabolite:0x00005645c9de4b48>

3D Structure for #<Metabolite:0x00005645c9de4b48>