MiMeDB: Showing metabocard for D-erythronate (MMDBc0055858)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:08:57 UTC

Update Date

2025-10-07 16:09:25 UTC

Metabolite ID

MMDBc0055858

Metabolite Identification

Common Name

D-erythronate

Description

D-erythronate is a four-carbon sugar alcohol belonging to the class of metabolites known as sugar acids. Its chemical structure features a hydroxyl group on each of the four carbon atoms, making it a diastereomer of D-threonate. D-erythronate is primarily involved in catabolic pathways, particularly in the metabolism of N-acetyl-d-glucosamine, a nutritional supplement linked to joint health (PMID:38157628 ). The catabolic pathways for D-erythronate have been characterized in various bacterial species, notably within the phyla Actinomycetota, Cyanobacteriota, Bacillota, Pseudomonadota, and Bacteroidota (PMID:38157628 ). In Brucella, a virulence-related DeoR-family transcriptional regulator (VdtR) has been identified that negatively regulates the erythronate metabolic pathway, promoting the bacterium's extracellular proliferation by utilizing D-erythronate, an oxidative product of erythritol (PMID:37671873 ). Furthermore, studies indicate that D-erythronate and other acid sugars share similar enzymatic catalysis and catabolic pathways, highlighting its relevance in microbial metabolism (PMID:30316512 ). Despite its significance, the detailed catabolism of D-erythronate remains sparsely reported in the literature (PMID:38157628 ).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
D-Erythronic acid	Generator

Molecular Formula

C₄H₇O₅

Average Mass

135.096

Monoisotopic Mass

135.029896905

IUPAC Name

(2R,3R)-2,3,4-trihydroxybutanoate

Traditional Name

(2R,3R)-2,3,4-trihydroxybutanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C4H8O5/c5-1-2(6)3(7)4(8)9/h2-3,5-7H,1H2,(H,8,9)/p-1/t2-,3-/m1/s1

InChI Key

JPIJQSOTBSSVTP-PWNYCUMCSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Short-chain hydroxy acid
Sugar acid
Hydroxy acid
Monosaccharide
Fatty acid
Secondary alcohol
1,2-diol
Carboxylic acid salt
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Primary alcohol
Alcohol
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.1	ChemAxon
pKa (Strongest Acidic)	3.4	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	100.82 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	37.18 m³·mol⁻¹	ChemAxon
Polarizability	11.13 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	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-erythronate_TMS_1	C[Si](C)(C)O[C@H](CO)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	2113.95
Gas Chromatography	D-erythronate_TMS_2	C[Si](C)(C)OC[C@@H](O)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	2022.28
Gas Chromatography	D-erythronate_TMS_3	C[Si](C)(C)O[C@@H](C(=O)[O-])[C@H](O)CO	standard non polar	2025-10-24	2362.16
Gas Chromatography	D-erythronate_TMS_4	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	2108.74
Gas Chromatography	D-erythronate_TMS_5	C[Si](C)(C)O[C@H](CO)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	2031.32
Gas Chromatography	D-erythronate_TMS_6	C[Si](C)(C)OC[C@@H](O)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	2075.45
Gas Chromatography	D-erythronate_TMS_7	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1576.77
Gas Chromatography	D-erythronate_TMS_1	C[Si](C)(C)O[C@H](CO)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	1998.55
Gas Chromatography	D-erythronate_TMS_2	C[Si](C)(C)OC[C@@H](O)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	1985.25
Gas Chromatography	D-erythronate_TMS_3	C[Si](C)(C)O[C@@H](C(=O)[O-])[C@H](O)CO	standard polar	2025-10-24	2466.5
Gas Chromatography	D-erythronate_TMS_4	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	2068.48
Gas Chromatography	D-erythronate_TMS_5	C[Si](C)(C)O[C@H](CO)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	1582.84
Gas Chromatography	D-erythronate_TMS_6	C[Si](C)(C)OC[C@@H](O)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2073.59
Gas Chromatography	D-erythronate_TMS_7	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2462.22

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	Firmicutes	1
Bacteria/Eubacteria	Proteobacteria	2	Human

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

20171439

KEGG Compound ID

Not Available

BioCyc ID

CPD-19877

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

20849007

PDB ID

Not Available

ChEBI ID

136591

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 D-erythronate (MMDBc0055858)

MOL for #<Metabolite:0x00007fadd4042638>

3D MOL for #<Metabolite:0x00007fadd4042638>

3D SDF for #<Metabolite:0x00007fadd4042638>

3D-SDF for #<Metabolite:0x00007fadd4042638>

PDB for #<Metabolite:0x00007fadd4042638>

3D PDB for #<Metabolite:0x00007fadd4042638>

SMILES for #<Metabolite:0x00007fadd4042638>

INCHI for #<Metabolite:0x00007fadd4042638>

Structure for #<Metabolite:0x00007fadd4042638>

3D Structure for #<Metabolite:0x00007fadd4042638>