MiMeDB: Showing metabocard for 2-Dehydro-3-deoxy-D-gluconate (MMDBc0049977)

Pharmaceutical

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:47:28 UTC

Update Date

2025-10-07 16:08:15 UTC

Metabolite ID

MMDBc0049977

Metabolite Identification

Common Name

2-Dehydro-3-deoxy-D-gluconate

Description

2-Dehydro-3-deoxy-D-gluconate is a carbohydrate metabolite belonging to the class of sugar acids. Its chemical structure features a dehydrogenated and deoxygenated form of D-gluconate, which plays a role in various metabolic pathways. This compound is involved in energy metabolism and has been identified among key metabolites in seminal plasma, highlighting its potential significance in metabolic processes. For instance, a study identified 2-dehydro-3-deoxy-D-gluconate alongside other metabolites such as D-Fructose and succinate, emphasizing its presence in the metabolic landscape of Liang guang Small-spotted pig and Duroc seminal plasma (PMID:36686181 ). Furthermore, the enzyme 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (KduD), encoded by the kduD gene, is crucial for the biotransformation of 11-DOC, indicating a specific enzymatic pathway in which this metabolite is involved (PMID:24509771 ). Overall, 2-dehydro-3-deoxy-D-gluconate serves as an important intermediary in carbohydrate metabolism and enzymatic reactions.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₆H₁₀O₆

Average Mass

178.14

Monoisotopic Mass

178.047738052

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

Not Available

InChI Identifier

InChI=1S/C6H10O6/c7-2-5(10)3(8)1-4(9)6(11)12/h3,5,7-8,10H,1-2H2,(H,11,12)/t3-,5+/m0/s1

InChI Key

WPAMZTWLKIDIOP-WVZVXSGGSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Not Available

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	341.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	270.5
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	45.5
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	246.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	272.3
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	312.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	723.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	668.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	842.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	161.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	312.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	178.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	41.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	357.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	633.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	63.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	210.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	854.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	592.5

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_1	C[Si](C)(C)O[C@H](CO)[C@@H](O)CC(=O)C(=O)O	standard non polar	2025-10-24	2254.18
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_2	C[Si](C)(C)OC[C@@H](O)[C@@H](O)CC(=O)C(=O)O	standard non polar	2025-10-24	1665.51
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_3	C[Si](C)(C)O[C@@H](CC(=O)C(=O)O)[C@H](O)CO	standard non polar	2025-10-24	1933.98
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_4	C[Si](C)(C)OC(=O)C(=O)C[C@H](O)[C@H](O)CO	standard non polar	2025-10-24	1513.81
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_5	C[Si](C)(C)OC(=C[C@H](O)[C@H](O)CO)C(=O)O	standard non polar	2025-10-24	1986.85
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_6	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)CC(=O)C(=O)O	standard non polar	2025-10-24	2000.03
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_7	C[Si](C)(C)O[C@@H](CC(=O)C(=O)O)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	2003.99
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_8	C[Si](C)(C)OC(=O)C(=O)C[C@H](O)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	1915.65
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_9	C[Si](C)(C)OC(=C[C@H](O)[C@@H](CO)O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	2140.56
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_10	C[Si](C)(C)OC[C@@H](O)[C@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	2054.98
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_11	C[Si](C)(C)OC[C@@H](O)[C@@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1814.4
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_12	C[Si](C)(C)OC[C@@H](O)[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1729.91
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_13	C[Si](C)(C)OC(=O)C(=O)C[C@H](O[Si](C)(C)C)[C@H](O)CO	standard non polar	2025-10-24	1645.36
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_14	C[Si](C)(C)OC(=C[C@H](O[Si](C)(C)C)[C@H](O)CO)C(=O)O	standard non polar	2025-10-24	1456.32
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_15	C[Si](C)(C)OC(=O)C(=C[C@H](O)[C@H](O)CO)O[Si](C)(C)C	standard non polar	2025-10-24	1780.99
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_16	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	1960.5
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_17	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2079.67
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_18	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	2114.37
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_19	C[Si](C)(C)OC(=O)C(=O)C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	2081.35
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_20	C[Si](C)(C)OC(=C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1582.07
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_21	C[Si](C)(C)OC(=O)C(=C[C@H](O)[C@@H](CO)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1377.11
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_22	C[Si](C)(C)OC[C@@H](O)[C@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1462.31
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_23	C[Si](C)(C)OC[C@@H](O)[C@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	2332.77
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_24	C[Si](C)(C)OC[C@@H](O)[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2189.65
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_25	C[Si](C)(C)OC(=O)C(=C[C@H](O[Si](C)(C)C)[C@H](O)CO)O[Si](C)(C)C	standard non polar	2025-10-24	1854.38
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_26	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1614.22
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_27	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard non polar	2025-10-24	2188.51
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_28	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2323.0
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_29	C[Si](C)(C)OC(=O)C(=C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2893.22
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_30	C[Si](C)(C)OC[C@@H](O)[C@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1648.99
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_31	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1862.75
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_1	C[Si](C)(C)O[C@H](CO)[C@@H](O)CC(=O)C(=O)O	standard polar	2025-10-24	2174.84
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_2	C[Si](C)(C)OC[C@@H](O)[C@@H](O)CC(=O)C(=O)O	standard polar	2025-10-24	1997.37
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_3	C[Si](C)(C)O[C@@H](CC(=O)C(=O)O)[C@H](O)CO	standard polar	2025-10-24	2479.58
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_4	C[Si](C)(C)OC(=O)C(=O)C[C@H](O)[C@H](O)CO	standard polar	2025-10-24	1835.07
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_5	C[Si](C)(C)OC(=C[C@H](O)[C@H](O)CO)C(=O)O	standard polar	2025-10-24	2524.39
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_6	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)CC(=O)C(=O)O	standard polar	2025-10-24	2284.47
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_7	C[Si](C)(C)O[C@@H](CC(=O)C(=O)O)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	2335.12
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_8	C[Si](C)(C)OC(=O)C(=O)C[C@H](O)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	1927.59
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_9	C[Si](C)(C)OC(=C[C@H](O)[C@@H](CO)O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	1950.54
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_10	C[Si](C)(C)OC[C@@H](O)[C@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	2275.42
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_11	C[Si](C)(C)OC[C@@H](O)[C@@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1614.29
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_12	C[Si](C)(C)OC[C@@H](O)[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2220.21
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_13	C[Si](C)(C)OC(=O)C(=O)C[C@H](O[Si](C)(C)C)[C@H](O)CO	standard polar	2025-10-24	1774.43
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_14	C[Si](C)(C)OC(=C[C@H](O[Si](C)(C)C)[C@H](O)CO)C(=O)O	standard polar	2025-10-24	1757.42
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_15	C[Si](C)(C)OC(=O)C(=C[C@H](O)[C@H](O)CO)O[Si](C)(C)C	standard polar	2025-10-24	2228.55
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_16	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](CC(=O)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	2107.01
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_17	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)CC(=O)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2184.14
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_18	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	1402.19
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_19	C[Si](C)(C)OC(=O)C(=O)C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	2186.32
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_20	C[Si](C)(C)OC(=C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	1595.59
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_21	C[Si](C)(C)OC(=O)C(=C[C@H](O)[C@@H](CO)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2559.19
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_22	C[Si](C)(C)OC[C@@H](O)[C@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1975.84
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_23	C[Si](C)(C)OC[C@@H](O)[C@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	1317.68
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_24	C[Si](C)(C)OC[C@@H](O)[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2299.69
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_25	C[Si](C)(C)OC(=O)C(=C[C@H](O[Si](C)(C)C)[C@H](O)CO)O[Si](C)(C)C	standard polar	2025-10-24	1481.22
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_26	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](CC(=O)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2425.7
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_27	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](C=C(O[Si](C)(C)C)C(=O)O)O[Si](C)(C)C	standard polar	2025-10-24	2792.68
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_28	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2015.24
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_29	C[Si](C)(C)OC(=O)C(=C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1384.86
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_30	C[Si](C)(C)OC[C@@H](O)[C@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2294.61
Gas Chromatography	2-Dehydro-3-deoxy-D-gluconate_TMS_31	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](C=C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1703.84

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

Microbial Pathways

Pathways

Name	SMPDB/PathBank	Species
D-Glucuronate degradation		Escherichia coli Escherichia coli SMS-3-5 Escherichia coli UTI89 Escherichia coli 55989 Escherichia coli SE11 Pseudomonas aeruginosa PA7 Actinobacillus succinogenes 130Z Escherichia coli CFT073 Ochrobactrum anthropi Bacillus subtilis Pseudomonas stutzeri Klebsiella pneumoniae Pseudomonas fluorescens Pf-5 Bacillus amyloliquefaciens Roseburia intestinalis L1-82 Clostridium saccharoperbutylacetonicum N1-4(HMT) Salmonella enterica Clostridium acetobutylicum ATCC 824 Saccharopolyspora erythraea NRRL 2338 Anaerococcus prevotii DSM 20548 Bacillus halodurans C-125 Alkalihalobacillus pseudofirmus OF4 Bacillus timonensis 10403023 Bacteroides caccae Bacteroides cellulosilyticus Bacteroides eggerthii Bacteroides ovatus Bacteroides stercoris Bacteroides stercoris ATCC 43183 Bacteroides thetaiotaomicron Bacteroides thetaiotaomicron VPI-5482 Bacteroides vulgatus Bacteroides xylanisolvens XB1A Blautia hansenii DSM 20583 Brevibacillus brevis NBRC 100599 Clostridium beijerinckii NCIMB 8052 Clostridium saccharolyticum Collinsella aerofaciens Dorea formicigenerans ATCC 27755 Dysgonomonas gadei ATCC BAA-286 Enterococcus faecalis Eubacterium eligens ATCC 27750 Lactobacillus paracasei Megamonas hypermegale Methylobacterium nodulans Ochrobactrum anthropi ATCC 49188 Ochrobactrum intermedium LMG 3301 Parabacteroides goldsteinii dnLKV18 Prevotella ruminicola 23 Roseburia hominis A2-183 Burkholderia cepacia Pseudomonas fluorescens Pseudomonas syringae Xanthomonas campestris Bradyrhizobium japonicum Mesorhizobium loti Sinorhizobium meliloti Citrobacter koseri Shigella boydii Shigella dysenteriae Shigella flexneri Shigella sonnei Vibrio vulnificus Bacteroides uniformis Ruminococcus albus Streptococcus uberis Enterococcus gallinarum Bacillus licheniformis Priestia megaterium Bacillus pumilus Clostridium butyricum Lactobacillus delbrueckii Lactobacillus sakei Cellulomonas flavigena Corynebacterium glutamicum Mycobacterium avium Thermotoga neapolitana Roseobacter denitrificans Acidothermus cellulolyticus Caldicellulosiruptor bescii Enterococcus casseliflavus Eubacterium eligens Eubacterium ramulus Actinosynnema mirum Caldicellulosiruptor saccharolyticus Enterococcus cecorum Mitsuokella multacida Brachyspira pilosicoli Enterococcus durans Blautia hydrogenotrophica Burkholderia vietnamiensis Holdemania filiformis Enterobacter cancerogenus Bacillus clausii Bacillus pseudofirmus Achromobacter xylosoxidans Burkholderia multivorans Burkholderia cenocepacia Citrobacter youngae Burkholderia ambifaria Prevotella copri Marvinbryantia formatexigens Alicycliphilus denitrificans Bacteroides massiliensis Escherichia albertii Subdoligranulum variabile Bacteroides nordii Bacteroides plebeius Phocaeicola coprocola Bacteroides intestinalis Bacteroides salanitronis Bacteroides fluxus Bacteroides oleiciplenus Bacteroides faecis Agrobacterium tumefaciens Alistipes shahii Bacteroides xylanisolvens Blautia hansenii Clostridium beijerinckii Dorea formicigenerans Dysgonomonas gadei Enterococcus faecium Klebsiella variicola Lactobacillus rhamnosus Lactococcus lactis Parabacteroides goldsteinii Prevotella ruminicola Achromobacter xylosoxidans A8 Actinobacillus pleuropneumoniae serovar 5b str. L20 Actinobacillus pleuropneumoniae serovar 3 str. JL03 Actinobacillus pleuropneumoniae serovar 7 str. AP76 Agrobacterium tumefaciens str. C58 Arcanobacterium haemolyticum DSM 20595 Bacillus megaterium QM B1551 Bacillus licheniformis ATCC 14580 Bacillus clausii KSM-K16 Bacillus amyloliquefaciens FZB42 Bacillus pumilus SAFR-032 Priestia megaterium DSM 319 Bacillus subtilis subsp. spizizenii str. W23 Bacillus amyloliquefaciens DSM 7 Bradyrhizobium japonicum USDA 110 Citrobacter koseri ATCC BAA-895 Cronobacter sakazakii ATCC BAA-894 Delftia acidovorans SPH-1 Dyadobacter fermentans DSM 18053 Enterobacter cloacae subsp. cloacae ATCC 13047 Escherichia coli APEC O1 Escherichia coli E24377A Escherichia coli O127:H6 str. E2348/69 Escherichia coli UMN026 Escherichia fergusonii ATCC 35469 Escherichia coli ED1a Escherichia coli IAI39 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 Lactobacillus brevis ATCC 367 Lactobacillus casei ATCC 334 Lactococcus lactis subsp. lactis Il1403 Lactococcus lactis subsp. cremoris SK11 Lactococcus lactis subsp. cremoris MG1363 Mesorhizobium loti MAFF303099 Mycobacterium avium subsp. paratuberculosis K-10 Mycobacterium avium 104 Escherichia coli 042 Edwardsiella tarda FL6-60 Pseudomonas fluorescens Pf0-1 Pseudomonas stutzeri A1501 Pseudomonas fluorescens SBW25 Rhizobium leguminosarum bv. viciae 3841 Rhizobium leguminosarum bv. trifolii WSM2304 Rhodococcus erythropolis PR4 Ruminococcus albus 7 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Salmonella enterica subsp. enterica serovar Newport str. SL254 Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 Salmonella enterica subsp. enterica serovar Agona str. SL483 Salmonella enterica subsp. enterica serovar Dublin str. CT02021853 Shigella sonnei Ss046 Shigella flexneri 5 str. 8401 Spirosoma linguale DSM 74 Staphylococcus haemolyticus JCSC1435 Streptococcus uberis 0140J Vibrio parahaemolyticus RIMD 2210633 Yersinia enterocolitica subsp. enterocolitica 8081 Yersinia pseudotuberculosis IP 31758 Bacteroides cellulosilyticus DSM 14838 Bacteroides eggerthii 1_2_48FAA Bacteroides fluxus YIT 12057 Bacteroides graminisolvens Bacteroides graminisolvens DSM 19988 = JCM 15093 Bacteroides intestinalis DSM 17393 Bacteroides nordii CL02T12C05 Bacteroides oleiciplenus YIT 12058 Bacteroides ovatus ATCC 8483 Bacteroides uniformis ATCC 8492 Bacteroides xylanisolvens SD CC 1b Bacteroides sp. 1_1_14 Bacteroides sp. 1_1_30 Bacteroides sp. 2_1_22 Bacteroides sp. 2_2_4 Bacteroides sp. D2 Bacteroides sp. D20 Bacteroides sp. D22 Odoribacter laneus YIT 12061 Paraprevotella clara YIT 11840 Paraprevotella xylaniphila YIT 11841 Prevotella buccae ATCC 33574 Prevotella salivae DSM 15606 Parabacteroides johnsonii DSM 18315 Bacteroides dorei DSM 17855 Spirosoma linguale Cetobacterium somerae ATCC BAA-474 Rhizobium etli Azorhizobium caulinodans Xanthobacter autotrophicus Burkholderia cepacia GG4 Succinatimonas hippei Succinatimonas hippei YIT 12066 Succinivibrio dextrinosolvens Cedecea davisae Cedecea davisae DSM 4568 Citrobacter amalonaticus Citrobacter amalonaticus Y19 Citrobacter freundii Citrobacter youngae ATCC 29220 Enterobacter hormaechei Escherichia albertii TW07627 Klebsiella aerogenes Salmonella Salmonella enterica subsp. enterica serovar Typhimurium Trabulsiella guamensis Trabulsiella guamensis ATCC 49490 Edwardsiella tarda Edwardsiella tarda ATCC 23685 Hafnia alvei Hafnia alvei ATCC 51873 Morganella morganii Morganella morganii subsp. morganii KT Serratia marcescens subsp. marcescens Db11 Yersinia enterocolitica Yersinia pestis Yersinia pseudotuberculosis Actinobacillus pleuropneumoniae Vibrio fluvialis Vibrio fluvialis PG41 Vibrio parahaemolyticus Vibrio mimicus Brachyspira pilosicoli B2904 Trueperella pyogenes Rhodococcus erythropolis Brevibacterium linens Microbacterium oleivorans Kocuria palustris PEL Cellulosimicrobium cellulans Propionibacterium Thermomonospora curvata Olsenella profusa F0195 Collinsella tanakaei YIT 12063 Bacillus altitudinis Bacillus infantis NRRL B-14911 Bacillus firmus DS1 Listeria grayi Listeria grayi DSM 20601 Paenibacillus lactis 154 Exiguobacterium aurantiacum Enterococcus asini ATCC 700915 Enterococcus casseliflavus ATCC 12755 Enterococcus cecorum DSM 20682 = ATCC 43198 Enterococcus phoeniculicola ATCC BAA-412 Lactobacillus paracasei subsp. paracasei 8700:2 Lactobacillus rhamnosus LMS2-1 Lactobacillus coleohominis 101-4-CHN Lactobacillus coryniformis subsp. coryniformis CECT 5711 Pediococcus acidilactici DSM 20284 Weissella cibaria Butyricicoccus pullicaecorum Butyricicoccus pullicaecorum 1.2 Clostridium butyricum E4 str. BoNT E BL5262 Clostridium sartagoforme AAU1 Eubacterium ramulus ATCC 29099 Blautia hydrogenotrophica DSM 10507 Clostridium asparagiforme DSM 15981 [Clostridium] bolteae ATCC BAA-613 Clostridium citroniae WAL-17108 Lachnospira multipara [Ruminococcus] gnavus ATCC 29149 Roseburia inulinivorans DSM 16841 Flavonifractor plautii ATCC 29863 Pseudoflavonifractor capillosus ATCC 29799 Subdoligranulum variabile DSM 15176 [Bacteroides] pectinophilus ATCC 43243 Holdemania filiformis DSM 12042 Mitsuokella multacida DSM 20544 Megasphaera elsdenii Ralstonia eutropha H16 Xanthomonas campestris pv. campestris str. ATCC 33913 Xanthomonas campestris pv. campestris str. B100 Xanthomonas campestris pv. campestris str. 8004 Corynebacterium glutamicum ATCC 13032 Clostridioides difficile 630 Clostridioides difficile NAP08 Bifidobacterium longum subsp. infantis Lachnoclostridium phytofermentans ISDg Acidothermus cellulolyticus 11B Alkaliphilus metalliredigens QYMF Anoxybacillus flavithermus WK1 Arthrobacter sp. FB24 Arthrobacter aurescens TC1 Arthrobacter chlorophenolicus A6 Beutenbergia cavernae DSM 12333 Butyrivibrio proteoclasticus B316 Caldicellulosiruptor bescii DSM 6725 Cellulomonas flavigena DSM 20109 Clostridium cellulolyticum H10 Corynebacterium glutamicum R Deinococcus geothermalis DSM 11300 Exiguobacterium sp. AT1b Frankia sp. EuI1c Geobacillus kaustophilus HTA426 Geobacillus thermodenitrificans NG80-2 Intrasporangium calvum DSM 43043 Jonesia denitrificans DSM 20603 Kineococcus radiotolerans SRS30216 Kribbella flavida DSM 17836 Nakamurella multipartita DSM 44233 Oceanobacillus iheyensis HTE831 Caldicellulosiruptor saccharolyticus DSM 8903 Renibacterium salmoninarum ATCC 33209 Rhodococcus opacus B4 Rhodococcus jostii RHA1 Saccharomonospora viridis DSM 43017 Sanguibacter keddieii DSM 10542 Streptomyces violaceusniger Tu 4113 Streptosporangium roseum DSM 43021 Thermoanaerobacter sp. X514 Thermoanaerobacter pseudethanolicus ATCC 33223 Thermoanaerobacter italicus Ab9 Thermoanaerobacterium thermosaccharolyticum DSM 571 Thermomonospora curvata DSM 43183 Xylanimonas cellulosilytica DSM 15894 Aspergillus nomiae NRRL 13137 Aspergillus novofumigatus Aspergillus novofumigatus IBT 16806 Aspergillus parasiticus SU-1 Aspergillus phoenicis Aspergillus ruber Aspergillus sclerotioniger Aspergillus glaucus Aspergillus aculeatus ATCC 16872 Aspergillus leporis Aspergillus niger ATCC 1015 Aspergillus oryzae RIB40 Aspergillus terreus NIH2624 Aspergillus wentii Aspergillus clavatus NRRL 1 Aspergillus fischeri NRRL 181 Aspergillus fumigatus A1163 Aspergillus fumigatus Af293 Aspergillus calidoustus Aspergillus nidulans FGSC A4 Aspergillus taichungensis Aspergillus tamarii Aspergillus thermomutatus Aspergillus tubingensis Aspergillus violaceofuscus Aspergillus viridinutans Penicillium brasilianum Penicillium brevicompactum Penicillium canescens Penicillium chermesinum Penicillium citrinum Penicillium concentricum Penicillium daleae Penicillium decumbens Penicillium griseofulvum Penicillium hordei Penicillium italicum Penicillium nalgiovense Penicillium oxalicum Penicillium polonicum Penicillium roqueforti FM164 Penicillium solitum Penicillium steckii Penicillium thymicola Penicillium vulpinum Verticillium alfalfae VaMs.102 Trichoderma asperellum Trichoderma citrinoviride Trichoderma parareesei Trichoderma reesei QM6a Fusarium acutatum Fusarium fujikuroi IMI 58289 Fusarium mangiferae Fusarium nygamai Fusarium proliferatum ET1 Fusarium subglutinans Fusarium verticillioides 7600 Fusarium heterosporum Fusarium equiseti Fusarium oxysporum Fo5176 Fusarium oxysporum f. sp. lycopersici 4287 Fusarium austroamericanum Fusarium graminearum PH-1 Fusarium poae Fusarium pseudograminearum CS3096 Fusarium sporotrichioides Fusarium vanettenii Fusarium vanettenii 77-13-4 Fusarium tricinctum Paraburkholderia graminis C4D1M Acidipropionibacterium acidipropionici ATCC 4875 Bacteroides salanitronis DSM 18170 Klebsiella aerogenes KCTC 2190 Halanaerobium hydrogeniformans Acidobacterium capsulatum ATCC 51196 Agrobacterium vitis S4 Agrobacterium radiobacter K84 Alicycliphilus denitrificans K601 Azorhizobium caulinodans ORS 571 Azotobacter vinelandii DJ Mannheimia succiniciproducens MBEL55E Bordetella petrii DSM 12804 Brachyspira hyodysenteriae WA1 Brachyspira murdochii DSM 12563 Brachyspira pilosicoli 95/1000 Bradyrhizobium sp. BTAi1 Brucella melitensis bv. 1 str. 16M Brucella abortus bv. 1 str. 9-941 Brucella ovis ATCC 25840 Brucella canis ATCC 23365 Brucella suis ATCC 23445 Brucella abortus S19 Brucella melitensis ATCC 23457 Brucella microti CCM 4915 Burkholderia mallei ATCC 23344 Burkholderia pseudomallei 1710b Burkholderia sp. 383 Burkholderia xenovorans LB400 Burkholderia ambifaria AMMD Burkholderia mallei NCTC 10229 Burkholderia pseudomallei 1106a Burkholderia vietnamiensis G4 Burkholderia cenocepacia MC0-3 Burkholderia ambifaria MC40-6 Burkholderia phymatum STM815 Burkholderia phytofirmans PsJN Burkholderia cenocepacia J2315 Candidatus Koribacter versatilis Ellin345 Caulobacter crescentus CB15 Caulobacter crescentus NA1000 Caulobacter segnis ATCC 21756 Cellulophaga algicola DSM 14237 Clostridium lentocellum DSM 5427 Cellvibrio japonicus Ueda107 Chitinophaga pinensis DSM 2588 Chromohalobacter salexigens DSM 3043 Citrobacter rodentium ICC168 Cronobacter turicensis z3032 Cupriavidus taiwanensis LMG 19424 Deinococcus deserti VCD115 Dickeya dadantii Ech703 Dickeya zeae Ech1591 Dickeya dadantii Ech586 Dickeya dadantii 3937 Dinoroseobacter shibae DFL 12 Edwardsiella ictaluri 93-146 Enterobacter sp. 638 Enterobacter cloacae SCF1 Erwinia billingiae Eb661 Gluconacetobacter diazotrophicus PAl 5 Haliangium ochraceum DSM 14365 Halorhabdus utahensis DSM 12940 Haloterrigena turkmenica DSM 5511 Jannaschia sp. CCS1 Klebsiella pneumoniae 342 Leadbetterella byssophila DSM 17132 Leifsonia xyli subsp. xyli str. CTCB07 Maricaulis maris MCS10 Marinomonas mediterranea MMB-1 Marinomonas posidonica IVIA-Po-181 Methylobacterium nodulans ORS 2060 Microbacterium testaceum StLB037 Novosphingobium aromaticivorans DSM 12444 Xanthomonas axonopodis pv. citri str. 306 Sorangium cellulosum 'So ce 56' Alteromonas macleodii str. 'Deep ecotype' Rhodobacter capsulatus SB1003 Pantoea ananatis LMG 20103 Paracoccus denitrificans PD1222 Pectobacterium atrosepticum SCRI1043 Pectobacterium carotovorum subsp. carotovorum PC1 Pedobacter heparinus DSM 2366 Petrotoga mobilis SJ95 Phenylobacterium zucineum HLK1 Photobacterium profundum SS9 Photorhabdus luminescens subsp. laumondii TTO1 Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949 Pirellula staleyi DSM 6068 Polaromonas sp. JS666 Polaromonas naphthalenivorans CJ2 Pseudoalteromonas haloplanktis TAC125 Pseudomonas syringae pv. tomato str. DC3000 Pseudomonas syringae pv. phaseolicola 1448A Pseudomonas syringae pv. syringae B728a Pseudomonas fulva 12-X Psychromonas ingrahamii 37 Ralstonia solanacearum GMI1000 Rhizobium etli CFN 42 Rhizobium etli CIAT 652 Rhizobium leguminosarum bv. trifolii WSM1325 Rhodopirellula baltica SH 1 Rhodothermus marinus DSM 4252 Roseobacter denitrificans OCh 114 Roseobacter litoralis Och 149 Ruegeria pomeroyi DSS-3 Ruegeria sp. TM1040 Saccharophagus degradans 2-40 Salmonella enterica subsp. enterica serovar Paratyphi A str. Sebaldella termitidis ATCC 33386 Shigella flexneri 2a str. 301 Shigella boydii Sb227 Shigella boydii CDC 3083-94 Sinorhizobium meliloti 1021 Sinorhizobium medicae WSM419 Sphingobium japonicum UT26S Sphingomonas wittichii RW1 Sphingopyxis alaskensis RB2256 Teredinibacter turnerae T7901 Thermotoga petrophila RKU-1 Thermotoga sp. RQ2 Thermotoga neapolitana DSM 4359 Tolumonas auensis DSM 9187 Treponema brennaborense DSM 12168 Variovorax paradoxus EPS Verminephrobacter eiseniae EF01-2 Vibrio vulnificus CMCP6 Vibrio vulnificus YJ016 Xanthobacter autotrophicus Py2 Xanthomonas oryzae pv. oryzae KACC10331 Xanthomonas campestris pv. vesicatoria str. 85-10 Xanthomonas oryzae pv. oryzae PXO99A Zunongwangia profunda SM-A87 Sphingobacterium paucimobilis HER1398 Atlantibacter hermannii NBRC 105704 Klebsiella michiganensis KCTC 1686 Chania multitudinisentens RB-25 Hungatella hathewayi DSM 13479

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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/Eubacteria	Proteobacteria	187	Human feces; Human sputum; Human ; Human feces; pleural fluid plaque; bal; Human subgingival plaque; Pig	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	182	Human feces; Human ; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	85	Human feces; Human ; Human urine; Human gastric fluid; Human appendix biopsy; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	5	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	25	Human feces; Human ; Human nasopharyngeal swab; Human supragingival plaque	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria	Firmicutes	2	Human feces; Human ; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	2	Human feces; Pig	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria	Proteobacteria	5	Human feces; Human sputum; Human ; Human feces; pleural fluid plaque; bal; Human subgingival plaque; Pig	Metabolic reconstruction
Archaea/Archaea	Crenarchaeota	1		Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	3		Metabolic reconstruction
Bacteria/Eubacteria	Deinococcus-thermus	1
Archaea/Archaea	nah	1
Bacteria	Actinobacteria	1	Human feces; Human ; Human nasopharyngeal swab; Human supragingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Elusimicrobia	1
Bacteria/Eubacteria	Thermotogae	5

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

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

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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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 ]
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-Dehydro-3-deoxy-D-gluconate (MMDBc0049977)

MOL for #<Metabolite:0x00007f9acd54a7f8>

3D MOL for #<Metabolite:0x00007f9acd54a7f8>

3D SDF for #<Metabolite:0x00007f9acd54a7f8>

3D-SDF for #<Metabolite:0x00007f9acd54a7f8>

PDB for #<Metabolite:0x00007f9acd54a7f8>

3D PDB for #<Metabolite:0x00007f9acd54a7f8>

SMILES for #<Metabolite:0x00007f9acd54a7f8>

INCHI for #<Metabolite:0x00007f9acd54a7f8>

Structure for #<Metabolite:0x00007f9acd54a7f8>

3D Structure for #<Metabolite:0x00007f9acd54a7f8>