MiMeDB: Showing metabocard for 5-Keto-D-gluconate (MMDBc0029913)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:46:37 UTC

Update Date

2022-08-31 17:37:35 UTC

Metabolite ID

MMDBc0029913

Metabolite Identification

Common Name

5-Keto-D-gluconate

Description

5-Keto-D-gluconate is metabolized from glucose in certain bacterial species. It is an intermediate in L-idonate degradation and ketogluconate metabolism. 5-Keto-D-gluconate 5-reductase catalyzes the reversible reduction of 5-ketogluconate to D-gluconate. This is the second reaction of the L-idonate catabolic pathway after uptake of L-idonate into the cell. The enzyme specifically reduces 5-ketogluconate using either NADH or NADPH. The enzyme is also specific for D-gluconate oxidation using NADP as the coenzyme, NAD does not serve as a coenzyme.

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      29.083 -21.281   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      29.853 -22.615   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      29.083 -23.948   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      27.543 -23.948   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      26.773 -25.282   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.543 -26.616   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      27.543 -21.281   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      31.393 -22.615   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      29.853 -25.282   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      26.773 -22.615   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      25.233 -25.282   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      26.773 -27.950   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      29.083 -26.616   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
5-Dehydrogluconate	Kegg
5-Dehydrogluconic acid	Generator
5-Keto-D-gluconic acid	Generator
D-Lyxo-5-hexulosonic acid	MeSH
5-dehydro-D-Gluconate	HMDB
5-K-Gluconate	HMDB
5-Ketogluconate	HMDB
5K-Gluconate	HMDB
D-Tagaturonate	HMDB
D-Tagaturonic acid	HMDB
Hex-5-ulosonic acid	HMDB
Tagaturonate	HMDB

Molecular Formula

C₆H₁₀O₇

Average Mass

194.1394

Monoisotopic Mass

194.042652674

IUPAC Name

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

Traditional Name

D-xylo-5-hexulosonic acid

CAS Registry Number

3470-36-8

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/h3-5,7,9-11H,1H2,(H,12,13)

InChI Key

IZSRJDGCGRAUAR-UHFFFAOYSA-N

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
Beta-hydroxy acid
Hydroxy fatty acid
Acyloin
Alpha-hydroxy acid
Beta-hydroxy ketone
Monosaccharide
Fatty acyl
Fatty acid
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Polyol
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Primary alcohol
Organic oxygen compound
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	112 g/L	ALOGPS
logP	-2.5	ALOGPS
logP	-2.9	ChemAxon
logS	-0.24	ALOGPS
pKa (Strongest Acidic)	3.24	ChemAxon
pKa (Strongest Basic)	-3.3	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	37.43 m³·mol⁻¹	ChemAxon
Polarizability	16.14 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	splash10-0a4r-9700000000-f59ffae0d69336cb8cc4	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positive	splash10-000i-7003950000-3f7e60a112e0f1555d00	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
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-3290946cb89a4fbc1b1b	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-05fr-9000000000-23d4f183f614acea954b	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0kmi-9500000000-cfab98e30c16d8ef2899	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-0mbi-9600000000-03c7fe3855ff8696eeb6	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-2900000000-b8130bb1e44804377a86	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4i-9400000000-008b0e4521e31c46716b	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-3f56faf0b0019c6c4a8d	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-05n0-9600000000-2c6e108719e386327a7f	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4r-9200000000-211c04dafc34c15bcf8a	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-0e659f59929887b732ff	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-062m-6900000000-a7eb31be81d05c8a039a	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-07ko-9100000000-b4324554ac9ff03b8b73	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08fr-9000000000-d2b982cb529c548041ea	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00fr-9300000000-932ed2f2bd56edcbc115	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a6r-9100000000-28f9d98804ffc5575fc8	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-84b73104308b522447cd	2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-25	View Spectrum

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

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	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Colorectal cancer	HMDB	25037050
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	HMDB	27275383
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	25037050

External Links

HMDB ID

HMDB0011731

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB028411

KNApSAcK ID

Not Available

Chemspider ID

152

KEGG Compound ID

C01062

BioCyc ID

CPD-645

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

157

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 5-Keto-D-gluconate (MMDBc0029913)

MOL for #<Metabolite:0x00007fecb262e9d0>

3D MOL for #<Metabolite:0x00007fecb262e9d0>

3D SDF for #<Metabolite:0x00007fecb262e9d0>

3D-SDF for #<Metabolite:0x00007fecb262e9d0>

PDB for #<Metabolite:0x00007fecb262e9d0>

3D PDB for #<Metabolite:0x00007fecb262e9d0>

SMILES for #<Metabolite:0x00007fecb262e9d0>

INCHI for #<Metabolite:0x00007fecb262e9d0>

Structure for #<Metabolite:0x00007fecb262e9d0>

3D Structure for #<Metabolite:0x00007fecb262e9d0>