MiMeDB: Showing metabocard for 2-deoxy-5-keto-D-gluconic acid (MMDBc0049982)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:47:33 UTC

Update Date

2022-09-01 02:17:45 UTC

Metabolite ID

MMDBc0049982

Metabolite Identification

Common Name

2-deoxy-5-keto-D-gluconic acid

Description

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      29.128 -22.234   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      30.468 -23.004   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.794 -23.004   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      29.128 -20.695   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      31.802 -22.234   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      30.468 -24.543   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      26.460 -22.234   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      33.142 -23.004   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      31.802 -20.695   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      25.120 -23.004   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      26.460 -20.695   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      34.447 -22.248   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1                                                            
CONECT    5    2    8    9                                                  
CONECT    6    2                                                            
CONECT    7    3   10   11                                                  
CONECT    8    5   12                                                       
CONECT    9    5                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    8                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
2-Deoxy-5-keto-D-gluconic acid	ChEBI
5-Dehydro-2-deoxy-D-gluconic acid	ChEBI
DKH	ChEBI
5-Dehydro-2-deoxy-D-gluconate	Kegg
2-Deoxy-D-threo-hex-5-ulosonic acid	Kegg
2-Deoxy-5-keto-D-gluconate	Generator
2-Deoxy-D-threo-hex-5-ulosonate	Generator
2-Deoxy-D-gluc-5-ulosonate	Generator

Molecular Formula

C₆H₁₀O₆

Average Mass

178.14

Monoisotopic Mass

178.047738042

IUPAC Name

(3R,4S)-3,4,6-trihydroxy-5-oxohexanoic acid

Traditional Name

2-deoxy-5-keto-D-gluconic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H10O6/c7-2-4(9)6(12)3(8)1-5(10)11/h3,6-8,12H,1-2H2,(H,10,11)/t3-,6+/m1/s1

InChI Key

UCYNJPYWOSFBAT-CVYQJGLWSA-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
Fatty acyl
Fatty acid
Beta-hydroxy ketone
Monosaccharide
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Carboxylic acid derivative
Carboxylic acid
Polyol
Monocarboxylic acid or derivatives
Organic oxygen compound
Carbonyl group
Primary alcohol
Hydrocarbon derivative
Alcohol
Organooxygen compound
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid (CHEBI:27972 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	215 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.2	ChemAxon
logS	0.08	ALOGPS
pKa (Strongest Acidic)	3.82	ChemAxon
pKa (Strongest Basic)	-3.3	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	36.09 m³·mol⁻¹	ChemAxon
Polarizability	15.5 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_12) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-1900000000-6f2e7758620c0dba078e	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btc-9400000000-c968799b544830a42aa7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0596-9000000000-faf02e49f12d29fd86e7	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0690-4900000000-fa70518c21fd981c6de3	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0a4i-9500000000-7b1509e86bc4a98cbba3	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-87fbd2ce3c40a47dc8cc	2019-02-23	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
MMDBr0006923	2-deoxy-5-keto-D-gluconic acid	6-phosphonato-5-dehydro-2-deoxy-D-gluconate(3-)	Not Available		VMH	30371894

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	Actinobacteria	30	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Proteobacteria	41	Human ; Human feces; Human pleural fluid plaque; Human dental plaque; Human nasal swab	Metabolic reconstruction
Bacteria	Firmicutes	69	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	2	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction

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

C06892

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

441201

PDB ID

Not Available

ChEBI ID

27972

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for 2-deoxy-5-keto-D-gluconic acid (MMDBc0049982)

MOL for #<Metabolite:0x00007fece7d81b30>

3D MOL for #<Metabolite:0x00007fece7d81b30>

3D SDF for #<Metabolite:0x00007fece7d81b30>

3D-SDF for #<Metabolite:0x00007fece7d81b30>

PDB for #<Metabolite:0x00007fece7d81b30>

3D PDB for #<Metabolite:0x00007fece7d81b30>

SMILES for #<Metabolite:0x00007fece7d81b30>

INCHI for #<Metabolite:0x00007fece7d81b30>

Structure for #<Metabolite:0x00007fece7d81b30>

3D Structure for #<Metabolite:0x00007fece7d81b30>