MiMeDB: Showing metabocard for (4S)-4,6-Dihydroxy-2,5-dioxohexanoate (MMDBc0029951)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:48:04 UTC

Update Date

2022-08-31 17:37:55 UTC

Metabolite ID

MMDBc0029951

Metabolite Identification

Common Name

(4S)-4,6-Dihydroxy-2,5-dioxohexanoate

Description

(4S)-4,6-Dihydroxy-2,5-dioxohexanoate (2,5-Diketo-3-deoxy-D-gluconate or 3-Deoxy-D-glycero-2,5-hexodiulosonate) is involved in pentose and glucuronate interconversions. It is a substrate for 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase. This enzyme catalyzes the reduction of 2,5-diketo-3-deoxygluconate (DKII or 4,6-dihydroxy-2,5-dioxohexanoate) into 2-keto-3-deoxygluconate (KDG or 2-dehydro-3-deoxygluconate) with a concomitant oxidation of NADH. It is also a substrate for 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase. This enzyme catalyzes the isomerization of 5-dehydro-4-deoxy-D-glucuronate to 3-deoxy-D-glycero-2,5-hexodiulosonate.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    5    7                                                       
CONECT    3    1    5    8   13                                             
CONECT    4    1    6    9                                                  
CONECT    5    2    3   10                                                  
CONECT    6    4   11   12                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    6                                                            
CONECT   13    3                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
2,5-Diketo-3-deoxy-D-gluconate	ChEBI
3-Deoxy-D-glycero-2,5-hexodiulosonate	ChEBI
2,5-Diketo-3-deoxy-D-gluconic acid	Generator
3-Deoxy-D-glycero-2,5-hexodiulosonic acid	Generator
(4S)-4,6-Dihydroxy-2,5-dioxohexanoic acid	Generator
3-Deoxy-D-glycero-hexo-2,5-diulosonate	Generator

Molecular Formula

C₆H₈O₆

Average Mass

176.1241

Monoisotopic Mass

176.032087988

IUPAC Name

(4S)-4,6-dihydroxy-2,5-dioxohexanoic acid

Traditional Name

2,5-diketo-3-deoxy-D-gluconate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H8O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,7-8H,1-2H2,(H,11,12)/t3-/m0/s1

InChI Key

IBGYNIRCYXIAON-VKHMYHEASA-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
Acyloin
Alpha-keto acid
Beta-hydroxy ketone
Monosaccharide
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Primary alcohol
Alcohol
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

dioxo monocarboxylic acid (CHEBI:15623 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	66.7 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-1.3	ChemAxon
logS	-0.42	ALOGPS
pKa (Strongest Acidic)	2.74	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	111.9 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	35.47 m³·mol⁻¹	ChemAxon
Polarizability	14.89 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 (TMS_1_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a6r-1900000000-e5f902336ca480e75655	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4u-6900000000-07b7eea4bbc3a4cd1976	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9200000000-c942a7d5e812325a0079	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-056r-3900000000-74611e36a0771d4c94cc	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0abj-9600000000-80ec4c6b80d2c6bc4ba5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-ca64c9bfb85ab21c41a9	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum

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
MMDBr0014393	5-Dehydro-4-deoxy-D-glucuronate	(4S)-4,6-Dihydroxy-2,5-dioxohexanoate	4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase	Isomerization	RHEA	34755880
MMDBr0014427	2-Dehydro-3-deoxy-D-gluconate	(4S)-4,6-Dihydroxy-2,5-dioxohexanoate	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0016371	2-dehydro-3-deoxy-L-galactonic acid	(4S)-4,6-Dihydroxy-2,5-dioxohexanoate	2-dehydro-3-deoxy-L-galactonate 5-dehydrogenase	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	72	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Firmicutes	13	Human feces; Human
Bacteria	Bacteroidetes	3	Human ; Human feces
Bacteria	Actinobacteria	1
Bacteria	Verrucomicrobia	1
Bacteria/NULL	Bacteroidetes	1	Human ; Human feces

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

C04349

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440303

PDB ID

Not Available

ChEBI ID

15623

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 (4S)-4,6-Dihydroxy-2,5-dioxohexanoate (MMDBc0029951)

MOL for #<Metabolite:0x00007f5abc179be8>

3D MOL for #<Metabolite:0x00007f5abc179be8>

3D SDF for #<Metabolite:0x00007f5abc179be8>

3D-SDF for #<Metabolite:0x00007f5abc179be8>

PDB for #<Metabolite:0x00007f5abc179be8>

3D PDB for #<Metabolite:0x00007f5abc179be8>

SMILES for #<Metabolite:0x00007f5abc179be8>

INCHI for #<Metabolite:0x00007f5abc179be8>

Structure for #<Metabolite:0x00007f5abc179be8>

3D Structure for #<Metabolite:0x00007f5abc179be8>