MiMeDB: Showing metabocard for D-erythrose (MMDBc0054424)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:11:51 UTC

Update Date

2025-10-07 16:04:18 UTC

Metabolite ID

MMDBc0054424

Metabolite Identification

Common Name

D-erythrose

Description

D-erythrose is a pentose sugar belonging to the class of aldopentoses. Its chemical structure features a five-carbon backbone with an aldehyde group, making it a crucial intermediate in various metabolic pathways. D-erythrose is involved in the pentose phosphate pathway, where it plays a role in redox homeostasis and host response, as indicated by untargeted metabolomic profiling that identified D-erythrose 4-phosphate among other metabolites (PMID:40427288 ). Additionally, D-erythrose has been shown to improve stress tolerance in salt-sensitive maize varieties by promoting primary root length (PMID:41040158 ). It is also a product of photocatalytic treatments involving other aldopentoses, demonstrating its versatility in synthetic chemistry (PMID:40436901 ). Furthermore, D-erythrose 4-phosphate serves as a key precursor for the biosynthesis of tyrosol in Saccharomyces cerevisiae, with its flux determining the yield of this compound (PMID:39686978 ). The enzyme cascade involving D-erythrose isomerase and other related enzymes highlights its potential in ATP production from D-fructose (PMID:40143462 ). Overall, D-erythrose exemplifies the intricate connections between carbohydrate metabolism and various biochemical pathways.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Erythrose, (r,s)-isomer	MeSH
Erythrose, (S-(r,s))-isomer	MeSH
Erythrose, (R-(r,s))-isomer	MeSH
L-Threose	MeSH
Threose	MeSH
D-Threose	MeSH
Erythrose	MeSH
2,3,4-Trihydroxybutanal	MeSH

Molecular Formula

C₄H₈O₄

Average Mass

120.1039

Monoisotopic Mass

120.042258744

IUPAC Name

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

Traditional Name

erythrose

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C4H8O4/c5-1-3(7)4(8)2-6/h1,3-4,6-8H,2H2/t3-,4+/m0/s1

InChI Key

YTBSYETUWUMLBZ-IUYQGCFVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharides

Alternative Parents

Substituents

Monosaccharide
Beta-hydroxy aldehyde
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Short-chain aldehyde
Primary alcohol
Carbonyl group
Aldehyde
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

erythrose (CHEBI:27904 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	765 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-2.3	ChemAxon
logS	0.8	ALOGPS
pKa (Strongest Acidic)	12.19	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	25.42 m³·mol⁻¹	ChemAxon
Polarizability	10.66 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
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)	splash10-0le9-2920000000-7044bac9c4e165034e23	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 3 TMS)	splash10-0ldi-1930000000-1c2a8d3caa534a5a00f1	2014-06-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum

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	301.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	264.9
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	39.8
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	238.3
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	283.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	348.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	636.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	455.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	829.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	198.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	310.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	217.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	42.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	332.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	632.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	77.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	288.5
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	810.0
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	596.4

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-erythrose_TMS_1	C[Si](C)(C)O[C@H](CO)[C@@H](O)C=O	standard non polar	2025-10-24	2014.69
Gas Chromatography	D-erythrose_TMS_2	C[Si](C)(C)OC[C@@H](O)[C@@H](O)C=O	standard non polar	2025-10-24	2080.95
Gas Chromatography	D-erythrose_TMS_3	C[Si](C)(C)O[C@@H](C=O)[C@H](O)CO	standard non polar	2025-10-24	1924.92
Gas Chromatography	D-erythrose_TMS_4	C[Si](C)(C)OC=C(O)[C@H](O)CO	standard non polar	2025-10-24	1920.36
Gas Chromatography	D-erythrose_TMS_5	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)C=O	standard non polar	2025-10-24	1824.69
Gas Chromatography	D-erythrose_TMS_6	C[Si](C)(C)O[C@@H](C=O)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	2089.46
Gas Chromatography	D-erythrose_TMS_7	C[Si](C)(C)OC=C(O)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	2109.72
Gas Chromatography	D-erythrose_TMS_8	C[Si](C)(C)OC[C@@H](O)[C@H](C=O)O[Si](C)(C)C	standard non polar	2025-10-24	1994.35
Gas Chromatography	D-erythrose_TMS_9	C[Si](C)(C)OC=C(O)[C@H](O)CO[Si](C)(C)C	standard non polar	2025-10-24	2084.87
Gas Chromatography	D-erythrose_TMS_10	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@H](O)CO	standard non polar	2025-10-24	2012.4
Gas Chromatography	D-erythrose_TMS_11	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](C=O)O[Si](C)(C)C	standard non polar	2025-10-24	2028.3
Gas Chromatography	D-erythrose_TMS_12	C[Si](C)(C)OC=C(O)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	1653.67
Gas Chromatography	D-erythrose_TMS_13	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C	standard non polar	2025-10-24	2162.52
Gas Chromatography	D-erythrose_TMS_14	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@H](O)CO[Si](C)(C)C	standard non polar	2025-10-24	1468.15
Gas Chromatography	D-erythrose_TMS_15	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2408.19
Gas Chromatography	D-erythrose_TMS_1	C[Si](C)(C)O[C@H](CO)[C@@H](O)C=O	standard polar	2025-10-24	2090.83
Gas Chromatography	D-erythrose_TMS_2	C[Si](C)(C)OC[C@@H](O)[C@@H](O)C=O	standard polar	2025-10-24	1972.92
Gas Chromatography	D-erythrose_TMS_3	C[Si](C)(C)O[C@@H](C=O)[C@H](O)CO	standard polar	2025-10-24	2263.75
Gas Chromatography	D-erythrose_TMS_4	C[Si](C)(C)OC=C(O)[C@H](O)CO	standard polar	2025-10-24	2060.37
Gas Chromatography	D-erythrose_TMS_5	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)C=O	standard polar	2025-10-24	2214.47
Gas Chromatography	D-erythrose_TMS_6	C[Si](C)(C)O[C@@H](C=O)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	2037.89
Gas Chromatography	D-erythrose_TMS_7	C[Si](C)(C)OC=C(O)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	2016.39
Gas Chromatography	D-erythrose_TMS_8	C[Si](C)(C)OC[C@@H](O)[C@H](C=O)O[Si](C)(C)C	standard polar	2025-10-24	2259.05
Gas Chromatography	D-erythrose_TMS_9	C[Si](C)(C)OC=C(O)[C@H](O)CO[Si](C)(C)C	standard polar	2025-10-24	2466.95
Gas Chromatography	D-erythrose_TMS_10	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@H](O)CO	standard polar	2025-10-24	1813.93
Gas Chromatography	D-erythrose_TMS_11	C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](C=O)O[Si](C)(C)C	standard polar	2025-10-24	1860.96
Gas Chromatography	D-erythrose_TMS_12	C[Si](C)(C)OC=C(O)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1588.87
Gas Chromatography	D-erythrose_TMS_13	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C	standard polar	2025-10-24	1679.58
Gas Chromatography	D-erythrose_TMS_14	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@H](O)CO[Si](C)(C)C	standard polar	2025-10-24	2162.66
Gas Chromatography	D-erythrose_TMS_15	C[Si](C)(C)OC=C(O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2256.34

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	Thermotogae	1
Eukaryota/Fungi	Ascomycota	2

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

C00007412

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Erythrose

METLIN ID

Not Available

PubChem Compound

94176

PDB ID

Not Available

ChEBI ID

27904

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-erythrose (MMDBc0054424)

MOL for #<Metabolite:0x00007f9aac2c1c28>

3D MOL for #<Metabolite:0x00007f9aac2c1c28>

3D SDF for #<Metabolite:0x00007f9aac2c1c28>

3D-SDF for #<Metabolite:0x00007f9aac2c1c28>

PDB for #<Metabolite:0x00007f9aac2c1c28>

3D PDB for #<Metabolite:0x00007f9aac2c1c28>

SMILES for #<Metabolite:0x00007f9aac2c1c28>

INCHI for #<Metabolite:0x00007f9aac2c1c28>

Structure for #<Metabolite:0x00007f9aac2c1c28>

3D Structure for #<Metabolite:0x00007f9aac2c1c28>