MiMeDB: Showing metabocard for 2,5-Diketo-D-gluconate (MMDBc0029780)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:41:22 UTC

Update Date

2022-08-31 17:16:54 UTC

Metabolite ID

MMDBc0029780

Metabolite Identification

Common Name

2,5-Diketo-D-gluconate

Description

2,5-Diketo-D-gluconate is an intermediate in the synthesis of ascorbic acid. It is a substrate for the enzyme 2,5-diketo-D-gluconic acid reductase B. This enzyme catalyzes the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG) with the following reaction: 2-dehydro-D-gluconate + NADP+ = 2,5-didehydro-D-gluconate + NADPH.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08131209042D          

 15 14  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  1  1  0  0  0  0
  8  2  2  0  0  0  0
  3  9  1  6  0  0  0
  4 10  1  6  0  0  0
 11  5  2  0  0  0  0
 12  6  1  0  0  0  0
 13  6  2  0  0  0  0
  3 14  1  6  0  0  0
  4 15  1  6  0  0  0
M  CHG  1  12  -1
M  END
> <DATABASE_ID>
MMDBc0029780

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(C(=O)CO)[C@]([H])(O)C(=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h3-4,7,9-10H,1H2,(H,12,13)/p-1/t3-,4+/m1/s1

> <INCHI_KEY>
RXMWXENJQAINCC-DMTCNVIQSA-M

> <FORMULA>
C6H7O7

> <MOLECULAR_WEIGHT>
191.1156

> <EXACT_MASS>
191.019177578

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
15.10513295774124

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S)-3,4,6-trihydroxy-2,5-dioxohexanoate

> <ALOGPS_LOGP>
-1.14

> <JCHEM_LOGP>
-2.027202744333333

> <ALOGPS_LOGS>
-0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.792721942209434

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5240306368417036

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3278882311562272

> <JCHEM_POLAR_SURFACE_AREA>
134.96

> <JCHEM_REFRACTIVITY>
47.6498

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.73e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-diketo-D-gluconate

> <JCHEM_VEBER_RULE>
0

$$$$

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-1
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    7                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    4    9   14                                             
CONECT    4    3    5   10   15                                             
CONECT    5    4    6   11                                                  
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                                                            
CONECT   14    3                                                            
CONECT   15    4                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
2,5-Diketogluconate	ChEBI
2-Dehydro-L-idonate	ChEBI
D-Threo-2,5-hexodiulosonate	ChEBI
2,5-Diketogluconic acid	Generator
2-Dehydro-L-idonic acid	Generator
D-Threo-2,5-hexodiulosonic acid	Generator
2,5-Diketo-D-gluconic acid	Generator
2,5-dioxo-D-Gluconate	MeSH

Molecular Formula

C₆H₇O₇

Average Mass

191.1156

Monoisotopic Mass

191.019177578

IUPAC Name

(3S,4S)-3,4,6-trihydroxy-2,5-dioxohexanoate

Traditional Name

2,5-diketo-D-gluconate

CAS Registry Number

53736-12-2

SMILES

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

InChI Identifier

InChI=1S/C6H8O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h3-4,7,9-10H,1H2,(H,12,13)/p-1/t3-,4+/m1/s1

InChI Key

RXMWXENJQAINCC-DMTCNVIQSA-M

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2-oxo monocarboxylic acid anion (CHEBI:11449 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	173 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-2	ChemAxon
logS	-0.08	ALOGPS
pKa (Strongest Acidic)	2.52	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	134.96 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	47.65 m³·mol⁻¹	ChemAxon
Polarizability	15.11 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	splash10-0006-0900000000-66697df72cf11dbf7f41	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03ec-7900000000-97ebe6ed711475246178	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dl-9200000000-a963788665da60d07e0a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00ko-7900000000-eb51687ff97b29540276	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052r-9400000000-5a948ab5e28d4d5a185b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-60c5fc89ff115a2f2c2d	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

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
MMDBr0014386	2-Dehydro-D-gluconate	2,5-Diketo-D-gluconate	2,5-diketo-D-gluconic acid reductase A	Reduction	RHEA	34755880
MMDBr0015393	3-Keto-L-gulonic acid	2,5-Diketo-D-gluconate	2,5-diketo-D-gluconic acid reductase A	Reduction	RHEA	34755880
MMDBr0019088	Hydrogen Ion	NADP	Glyoxylate/hydroxypyruvate reductase B	Reduction	PathBank	31602464
MMDBr0019089	Hydrogen Ion	NADP	2,5-diketo-D-gluconic acid reductase B	Reduction	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	Proteobacteria	5	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Actinobacteria	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									HMDB

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

9548631

PDB ID

Not Available

ChEBI ID

11449

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 2,5-Diketo-D-gluconate (MMDBc0029780)

MOL for #<Metabolite:0x00007f5a80343078>

3D MOL for #<Metabolite:0x00007f5a80343078>

3D SDF for #<Metabolite:0x00007f5a80343078>

3D-SDF for #<Metabolite:0x00007f5a80343078>

PDB for #<Metabolite:0x00007f5a80343078>

3D PDB for #<Metabolite:0x00007f5a80343078>

SMILES for #<Metabolite:0x00007f5a80343078>

INCHI for #<Metabolite:0x00007f5a80343078>

Structure for #<Metabolite:0x00007f5a80343078>

3D Structure for #<Metabolite:0x00007f5a80343078>