MiMeDB: Showing metabocard for 2-Keto-3-deoxy-D-gluconic acid (MMDBc0000388)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:36:40 UTC

Update Date

2022-08-31 06:03:00 UTC

Metabolite ID

MMDBc0000388

Metabolite Identification

Common Name

2-Keto-3-deoxy-D-gluconic acid

Description

2-Keto-3-deoxy-D-gluconic acid, also known as 2-dehydro-3-deoxy-D-galactonate, belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain. 2-Keto-3-deoxy-D-gluconic acid exists in all living organisms, ranging from bacteria to humans. 2-Keto-3-deoxy-D-gluconic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make 2-keto-3-deoxy-D-gluconic acid a potential biomarker for the consumption of these foods. 2-Keto-3-deoxy-D-gluconic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on 2-Keto-3-deoxy-D-gluconic acid.

Structure

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

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       5.071  -8.817   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.405  -8.047   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       6.405  -6.507   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       7.738  -8.817   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       7.738 -10.357   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       9.072  -8.047   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.406  -8.817   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      10.406 -10.357   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      11.739  -8.047   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      11.739  -6.507   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.073  -8.817   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      14.406  -8.047   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
2-Dehydro-3-deoxy-D-galactonate	ChEBI
2-Dehydro-3-deoxy-D-galactonic acid	Generator
2-Keto-3-deoxy-D-gluconate	Generator
2-oxo-3-Deoxygalactonic acid	MeSH, HMDB
3-Deoxy-D-threo-hexulosonic acid	MeSH, HMDB

Molecular Formula

C₆H₁₀O₆

Average Mass

178.14

Monoisotopic Mass

178.047738052

IUPAC Name

(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid

Traditional Name

(4R,5R)-4,5,6-trihydroxy-2-oxohexanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5-/m1/s1

InChI Key

WPAMZTWLKIDIOP-NQXXGFSBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Medium-chain keto acids and derivatives

Direct Parent

Medium-chain keto acids and derivatives

Alternative Parents

Substituents

Medium-chain keto acid
Alpha-keto acid
Beta-hydroxy ketone
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Primary alcohol
Organooxygen compound
Organic oxygen compound
Carbonyl group
Alcohol
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid (CHEBI:17028 )
hexonic acid (CHEBI:17028 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	134 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-1.8	ChemAxon
logS	-0.12	ALOGPS
pKa (Strongest Acidic)	2.91	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	36.32 m³·mol⁻¹	ChemAxon
Polarizability	15.54 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0cnc-9200000000-ca7affd58ffff99e944a	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-0kbf-9015500000-ab605becee17a221c24e	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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03fu-1900000000-16261982c6a9c806a823	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01p6-7900000000-504d11f169911538cb06	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00dv-9200000000-8845066b3c1b409ba899	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3900000000-be420c7266318ce9735a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9400000000-fd920a23173f050b910a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-059f-9200000000-c9791ea5084cab37fd9f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0159-2900000000-2c431e61342e81eac473	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4l-9100000000-645c0f5045ea3864800f	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-e067af341d49549e302c	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01ox-6900000000-21416d75e74f20ddb83e	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0fkc-9400000000-222927084d2d04afb1d9	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006x-9000000000-f04ea2cb2c4b2183144d	2021-09-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013539	2-Keto-3-deoxy-D-gluconic acid	2-Dehydro-3-deoxy-D-galactonate 6-phosphate	2-dehydro-3-deoxygalactonokinase	Phosphorylation	RHEA	34755880
MMDBr0013540	2-Keto-3-deoxy-D-gluconic acid	2-Dehydro-3-deoxy-D-galactonate 6-phosphate	2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase	Phosphorylation	RHEA	34755880
MMDBr0013796	D-Galactonate	2-Keto-3-deoxy-D-gluconic acid	L-arabinonate dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0016236	2-Keto-3-deoxy-D-gluconic acid	D-Glyceraldehyde	2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase	Aldol addition (or reverse)	RHEA	34755880
MMDBr0018316	Galactonic acid	2-Keto-3-deoxy-D-gluconic acid	D-galactonate dehydratase	Hydration/dehydration of C-O bond	PathBank	31602464
MMDBr0018317	2-Keto-3-deoxy-D-gluconic acid	Hydrogen Ion	2-dehydro-3-deoxygalactonokinase	Phosphorylation	PathBank	31602464
MMDBr0018404	D-Mannonate	2-Keto-3-deoxy-D-gluconic acid	Mannonate dehydratase	Hydration/dehydration of C-O bond	PathBank	31602464
MMDBr0018405	D-Altronate	2-Keto-3-deoxy-D-gluconic acid	Altronate dehydratase	Hydration/dehydration of C-O bond	PathBank	31602464
MMDBr0018408	2-Keto-3-deoxy-D-gluconic acid	Hydrogen Ion	2-dehydro-3-deoxygluconokinase	Phosphorylation	PathBank	31602464

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	Bacteroidetes	2	Human feces; Human stool	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Actinobacteria	1	Human ; Human feces; Human sputum; Human saliva; Human supragingival plaque; Human subgingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Proteobacteria	46	Human ; Human feces
Archaea	Crenarchaeota	1
Archaea/Archaea	Euryarchaeota	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
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	29808030

External Links

HMDB ID

HMDB0001353

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022572

KNApSAcK ID

Not Available

Chemspider ID

168361

KEGG Compound ID

C01216

BioCyc ID

2-DEHYDRO-3-DEOXY-D-GLUCONATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6184

PubChem Compound

194024

PDB ID

Not Available

ChEBI ID

17028

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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-Keto-3-deoxy-D-gluconic acid (MMDBc0000388)

MOL for #<Metabolite:0x00007f5abc48e608>

3D MOL for #<Metabolite:0x00007f5abc48e608>

3D SDF for #<Metabolite:0x00007f5abc48e608>

3D-SDF for #<Metabolite:0x00007f5abc48e608>

PDB for #<Metabolite:0x00007f5abc48e608>

3D PDB for #<Metabolite:0x00007f5abc48e608>

SMILES for #<Metabolite:0x00007f5abc48e608>

INCHI for #<Metabolite:0x00007f5abc48e608>

Structure for #<Metabolite:0x00007f5abc48e608>

3D Structure for #<Metabolite:0x00007f5abc48e608>