MiMeDB: Showing metabocard for 3-dehydro-D-erythronate (MMDBc0055357)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:49:58 UTC

Update Date

2025-10-07 16:09:04 UTC

Metabolite ID

MMDBc0055357

Metabolite Identification

Common Name

3-dehydro-D-erythronate

Description

3-dehydro-D-erythronate is a carbohydrate metabolite. There is limited literature available on this compound, indicating that it may not be widely studied or characterized in the existing biomedical research.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
3-Dehydro-D-erythronate	ChEBI
3-Dehydro-L-threonate anion	ChEBI
3-Dehydro-D-erythronic acid	Generator
3-Dehydro-L-threonic acid anion	Generator
3-Dehydro-L-threonic acid	Generator

Molecular Formula

C₄H₅O₅

Average Mass

133.08

Monoisotopic Mass

133.014246841

IUPAC Name

(2R)-2,4-dihydroxy-3-oxobutanoate

Traditional Name

3-dehydro-L-threonate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C4H6O5/c5-1-2(6)3(7)4(8)9/h3,5,7H,1H2,(H,8,9)/p-1/t3-/m1/s1

InChI Key

SCSGVVIUUUPOOJ-GSVOUGTGSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Short-chain keto acids and derivatives

Direct Parent

Short-chain keto acids and derivatives

Alternative Parents

Substituents

Beta-keto acid
Short-chain keto acid
Acyloin
Monosaccharide
1,3-dicarbonyl compound
Alpha-hydroxy ketone
Secondary alcohol
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Primary alcohol
Organooxygen compound
Alcohol
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-oxo monocarboxylic acid anion (CHEBI:57958 )
hydroxy monocarboxylic acid anion (CHEBI:57958 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.5	ChemAxon
pKa (Strongest Acidic)	3.1	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	97.66 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	36.42 m³·mol⁻¹	ChemAxon
Polarizability	10.48 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

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	184.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	127.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	76.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	323.9
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	369.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	952.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	479.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	910.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	223.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	274.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	239.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	67.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	361.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	749.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	79.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	279.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	975.9
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	651.4

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	3-dehydro-D-erythronate_TMS_1	C[Si](C)(C)O[C@@H](C(=O)[O-])C(=O)CO	standard non polar	2025-10-24	1903.66
Gas Chromatography	3-dehydro-D-erythronate_TMS_2	C[Si](C)(C)OCC(=O)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	2071.84
Gas Chromatography	3-dehydro-D-erythronate_TMS_3	C[Si](C)(C)OC(CO)=C(O)C(=O)[O-]	standard non polar	2025-10-24	2134.32
Gas Chromatography	3-dehydro-D-erythronate_TMS_4	C[Si](C)(C)OC(=CO)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	1838.74
Gas Chromatography	3-dehydro-D-erythronate_TMS_5	C[Si](C)(C)OCC(=O)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1659.01
Gas Chromatography	3-dehydro-D-erythronate_TMS_6	C[Si](C)(C)OC(CO)=C(O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	2105.52
Gas Chromatography	3-dehydro-D-erythronate_TMS_7	C[Si](C)(C)OC(=CO)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1228.76
Gas Chromatography	3-dehydro-D-erythronate_TMS_8	C[Si](C)(C)OCC(O[Si](C)(C)C)=C(O)C(=O)[O-]	standard non polar	2025-10-24	1229.06
Gas Chromatography	3-dehydro-D-erythronate_TMS_9	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	2416.55
Gas Chromatography	3-dehydro-D-erythronate_TMS_10	C[Si](C)(C)OCC(O[Si](C)(C)C)=C(O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1816.51
Gas Chromatography	3-dehydro-D-erythronate_TMS_11	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1286.88
Gas Chromatography	3-dehydro-D-erythronate_TMS_1	C[Si](C)(C)O[C@@H](C(=O)[O-])C(=O)CO	standard polar	2025-10-24	2164.95
Gas Chromatography	3-dehydro-D-erythronate_TMS_2	C[Si](C)(C)OCC(=O)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	2168.88
Gas Chromatography	3-dehydro-D-erythronate_TMS_3	C[Si](C)(C)OC(CO)=C(O)C(=O)[O-]	standard polar	2025-10-24	1820.71
Gas Chromatography	3-dehydro-D-erythronate_TMS_4	C[Si](C)(C)OC(=CO)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	1703.68
Gas Chromatography	3-dehydro-D-erythronate_TMS_5	C[Si](C)(C)OCC(=O)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	1861.72
Gas Chromatography	3-dehydro-D-erythronate_TMS_6	C[Si](C)(C)OC(CO)=C(O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2200.69
Gas Chromatography	3-dehydro-D-erythronate_TMS_7	C[Si](C)(C)OC(=CO)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2036.15
Gas Chromatography	3-dehydro-D-erythronate_TMS_8	C[Si](C)(C)OCC(O[Si](C)(C)C)=C(O)C(=O)[O-]	standard polar	2025-10-24	2010.4
Gas Chromatography	3-dehydro-D-erythronate_TMS_9	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	2172.76
Gas Chromatography	3-dehydro-D-erythronate_TMS_10	C[Si](C)(C)OCC(O[Si](C)(C)C)=C(O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2295.99
Gas Chromatography	3-dehydro-D-erythronate_TMS_11	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2294.13

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

Microbial Pathways

Pathways

Not Available

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	10	Cattle ; Human ; Human feces
Bacteria	Proteobacteria	1	Cattle ; Human ; Human feces

Exposure Sources

Other Exposures

Source Type	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

26330983

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25201352

PDB ID

Not Available

ChEBI ID

57958

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

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 3-dehydro-D-erythronate (MMDBc0055357)

MOL for #<Metabolite:0x00007f9ad14088c8>

3D MOL for #<Metabolite:0x00007f9ad14088c8>

3D SDF for #<Metabolite:0x00007f9ad14088c8>

3D-SDF for #<Metabolite:0x00007f9ad14088c8>

PDB for #<Metabolite:0x00007f9ad14088c8>

3D PDB for #<Metabolite:0x00007f9ad14088c8>

SMILES for #<Metabolite:0x00007f9ad14088c8>

INCHI for #<Metabolite:0x00007f9ad14088c8>

Structure for #<Metabolite:0x00007f9ad14088c8>

3D Structure for #<Metabolite:0x00007f9ad14088c8>