MiMeDB: Showing metabocard for 3-Dehydro-2-deoxy-D-gluconate (MMDBc0029768)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:40:47 UTC

Update Date

2024-04-30 19:41:51 UTC

Metabolite ID

MMDBc0029768

Metabolite Identification

Common Name

3-Dehydro-2-deoxy-D-gluconate

Description

3-Dehydro-2-deoxy-D-gluconate is an intermediate in pectin degradation and is involved in carbohydrate metabolism as well as pentose and glucuronate interconversions. It is a substrate for the enzyme 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

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       5.541   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.875   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.127   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.207  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       8.208   0.770   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.875  -1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.874   2.310   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    7                                                       
CONECT    3    1    6    8                                                  
CONECT    4    2    6    9                                                  
CONECT    5    1   10   11                                                  
CONECT    6    3    4   12                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
3-Dehydro-2-deoxy-D-gluconic acid	Generator

Molecular Formula

C₆H₁₀O₆

Average Mass

178.14

Monoisotopic Mass

178.047738052

IUPAC Name

4,5,6-trihydroxy-3-oxohexanoic acid

Traditional Name

4,5,6-trihydroxy-3-oxohexanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h4,6-7,9,12H,1-2H2,(H,10,11)

InChI Key

CNLFCQPCBQQMHK-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
Sugar acid
Beta-keto acid
Acyloin
1,3-dicarbonyl compound
Beta-hydroxy ketone
Monosaccharide
Keto acid
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Polyol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Carbonyl group
Primary alcohol
Organic oxide
Hydrocarbon derivative
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	209 g/L	ALOGPS
logP	-2	ALOGPS
logP	-1.9	ChemAxon
logS	0.07	ALOGPS
pKa (Strongest Acidic)	3.75	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	36.24 m³·mol⁻¹	ChemAxon
Polarizability	15.51 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_2_10) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-2900000000-642decf396af7b5cc277	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-9500000000-1d75fdeb0386f041e732	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06r6-9100000000-910031343a7cd5b307a3	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-066r-6900000000-560ccb74a7e1bb8c5090	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ab9-9300000000-15062933572e0ceb3f15	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ab9-9000000000-4db43b76044f589b7e8f	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

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

C03926

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

627

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Meister I, Zhang P, Sinha A, Skold CM, Wheelock AM, Izumi T, Chaleckis R, Wheelock CE: High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology. Anal Chem. 2021 Mar 30;93(12):5248-5258. doi: 10.1021/acs.analchem.1c00203. Epub 2021 Mar 19. [PubMed:33739820 ]

Showing metabocard for 3-Dehydro-2-deoxy-D-gluconate (MMDBc0029768)

MOL for #<Metabolite:0x00007fdb40352708>

3D MOL for #<Metabolite:0x00007fdb40352708>

3D SDF for #<Metabolite:0x00007fdb40352708>

3D-SDF for #<Metabolite:0x00007fdb40352708>

PDB for #<Metabolite:0x00007fdb40352708>

3D PDB for #<Metabolite:0x00007fdb40352708>

SMILES for #<Metabolite:0x00007fdb40352708>

INCHI for #<Metabolite:0x00007fdb40352708>

Structure for #<Metabolite:0x00007fdb40352708>

3D Structure for #<Metabolite:0x00007fdb40352708>