MiMeDB: Showing metabocard for 2-Deoxygluconate (MMDBc0029771)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:41:01 UTC

Update Date

2022-08-31 17:16:50 UTC

Metabolite ID

MMDBc0029771

Metabolite Identification

Common Name

2-Deoxygluconate

Description

2-deoxygluconate is a hexose. It is a substrate for 2-deoxygluconate dehydrogenase (kduD or EC 1.1.1.125) and participates in the following reaction: 2-deoxy-D-gluconate + NAD+ = 3-dehydro-2-deoxy-D-gluconate + NADH + H+

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-1
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
2-Deoxygluconic acid	Generator

Molecular Formula

C₆H₁₁O₆

Average Mass

179.1479

Monoisotopic Mass

179.055563084

IUPAC Name

3,4,5,6-tetrahydroxyhexanoate

Traditional Name

3,4,5,6-tetrahydroxyhexanoate

CAS Registry Number

3442-69-1

SMILES

OCC(O)C(O)C(O)CC([O-])=O

InChI Identifier

InChI=1S/C6H12O6/c7-2-4(9)6(12)3(8)1-5(10)11/h3-4,6-9,12H,1-2H2,(H,10,11)/p-1

InChI Key

PALQXFMLVVWXFD-UHFFFAOYSA-M

Chemical Taxonomy

Description

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

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Medium-chain fatty acid
Hydroxy fatty acid
Beta-hydroxy acid
Fatty acyl
Fatty acid
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

a small molecule (DE-O-GLUCONATE )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	812 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.7	ChemAxon
logS	0.61	ALOGPS
pKa (Strongest Acidic)	3.99	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	121.05 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	47.77 m³·mol⁻¹	ChemAxon
Polarizability	15.69 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-015a-1900000000-3fe0d7399c1513892a0d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0292-6900000000-f2f359ad6788b98db32b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dm-9100000000-1fcac427916301786043	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03xr-3900000000-f92cc3559f7cae2a6b2e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-07vi-9800000000-ea599acf28668bbce510	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0btc-9200000000-a979c2b094ae4106ca91	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	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

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

22134426

PDB ID

Not Available

ChEBI ID

Not Available

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 ]

Showing metabocard for 2-Deoxygluconate (MMDBc0029771)

MOL for #<Metabolite:0x00007fecb9477798>

3D MOL for #<Metabolite:0x00007fecb9477798>

3D SDF for #<Metabolite:0x00007fecb9477798>

3D-SDF for #<Metabolite:0x00007fecb9477798>

PDB for #<Metabolite:0x00007fecb9477798>

3D PDB for #<Metabolite:0x00007fecb9477798>

SMILES for #<Metabolite:0x00007fecb9477798>

INCHI for #<Metabolite:0x00007fecb9477798>

Structure for #<Metabolite:0x00007fecb9477798>

3D Structure for #<Metabolite:0x00007fecb9477798>