MiMeDB: Showing metabocard for D-homoserine (MMDBc0055867)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:22 UTC

Update Date

2025-10-07 16:09:25 UTC

Metabolite ID

MMDBc0055867

Metabolite Identification

Common Name

D-homoserine

Description

D-homoserine is a member of the amino acid class, specifically a non-proteinogenic amino acid. Its chemical structure features a hydroxyl group and an amino group attached to a four-carbon backbone, which is characteristic of homoserine derivatives. D-homoserine plays a role in various biochemical pathways, particularly in the metabolism of amino acids in microorganisms. For instance, in *Escherichia coli*, D-homoserine metabolism is influenced by the YgeA enzyme, which functions as an amino acid racemase, affecting the levels of D-homoserine in the cell (PMID:36214408 ). Additionally, D-homoserine lactone is involved in quorum sensing, where its derivatives can modulate biofilm formation and the synthesis of extracellular polymeric substances (EPSs) (PMID:36870195 ). Furthermore, D-homoserine lactone has been shown to enhance the growth of perovskite (PVK) materials on uneven surfaces by promoting crystal growth and passivating defects (PMID:39306599 ). Its selective hydrolysis from racemic mixtures has also been explored in the context of bacterial esterase activity (PMID:38377656 ). Overall, D-homoserine is a significant metabolite in microbial amino acid metabolism and signaling pathways.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2R)-2-Amino-4-hydroxybutanoic acid	ChEBI
(2R)-2-Amino-4-hydroxybutanoate	Generator
Homoserine	MeSH
Homoserine L-isomer	MeSH
L Isomer OF homoserine	MeSH
L-Isomer OF homoserine	MeSH

Molecular Formula

C₄H₉NO₃

Average Mass

119.12

Monoisotopic Mass

119.058243154

IUPAC Name

(2R)-2-amino-4-hydroxybutanoic acid

Traditional Name

D-homoserine

CAS Registry Number

Not Available

SMILES

[H][C@@](N)(CCO)C(O)=O

InChI Identifier

InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m1/s1

InChI Key

UKAUYVFTDYCKQA-GSVOUGTGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Short-chain hydroxy acid
Fatty acid
1,3-aminoalcohol
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

homoserine (CHEBI:30654 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.8	ChemAxon
pKa (Strongest Acidic)	2.22	ChemAxon
pKa (Strongest Basic)	9.16	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	83.55 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	26.91 m³·mol⁻¹	ChemAxon
Polarizability	11.35 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_3_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	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	502.5
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	407.9
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	39.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	219.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (void)	2025-10-24	284.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	326.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	441.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	883.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	799.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	193.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	546.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	210.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	40.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	404.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	745.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	78.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	308.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	657.9
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	566.3

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-homoserine_TMS_1	C[Si](C)(C)OCC[C@@H](N)C(=O)O	standard non polar	2025-10-24	2069.68
Gas Chromatography	D-homoserine_TMS_2	C[Si](C)(C)OC(=O)[C@H](N)CCO	standard non polar	2025-10-24	1799.07
Gas Chromatography	D-homoserine_TMS_3	C[Si](C)(C)N[C@H](CCO)C(=O)O	standard non polar	2025-10-24	2167.96
Gas Chromatography	D-homoserine_TMS_4	C[Si](C)(C)OCC[C@@H](N)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2013.0
Gas Chromatography	D-homoserine_TMS_5	C[Si](C)(C)N[C@H](CCO[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1730.67
Gas Chromatography	D-homoserine_TMS_6	C[Si](C)(C)N[C@H](CCO)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1625.16
Gas Chromatography	D-homoserine_TMS_7	C[Si](C)(C)N([C@H](CCO)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	2002.39
Gas Chromatography	D-homoserine_TMS_8	C[Si](C)(C)N[C@H](CCO[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2226.0
Gas Chromatography	D-homoserine_TMS_9	C[Si](C)(C)OCC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1775.8
Gas Chromatography	D-homoserine_TMS_10	C[Si](C)(C)OC(=O)[C@@H](CCO)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2397.69
Gas Chromatography	D-homoserine_TMS_11	C[Si](C)(C)OCC[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1379.62
Gas Chromatography	D-homoserine_TMS_1	C[Si](C)(C)OCC[C@@H](N)C(=O)O	standard polar	2025-10-24	1975.11
Gas Chromatography	D-homoserine_TMS_2	C[Si](C)(C)OC(=O)[C@H](N)CCO	standard polar	2025-10-24	1885.94
Gas Chromatography	D-homoserine_TMS_3	C[Si](C)(C)N[C@H](CCO)C(=O)O	standard polar	2025-10-24	1969.74
Gas Chromatography	D-homoserine_TMS_4	C[Si](C)(C)OCC[C@@H](N)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2232.28
Gas Chromatography	D-homoserine_TMS_5	C[Si](C)(C)N[C@H](CCO[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2000.84
Gas Chromatography	D-homoserine_TMS_6	C[Si](C)(C)N[C@H](CCO)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1894.7
Gas Chromatography	D-homoserine_TMS_7	C[Si](C)(C)N([C@H](CCO)C(=O)O)[Si](C)(C)C	standard polar	2025-10-24	2609.33
Gas Chromatography	D-homoserine_TMS_8	C[Si](C)(C)N[C@H](CCO[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2316.73
Gas Chromatography	D-homoserine_TMS_9	C[Si](C)(C)OCC[C@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2284.47
Gas Chromatography	D-homoserine_TMS_10	C[Si](C)(C)OC(=O)[C@@H](CCO)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2042.83
Gas Chromatography	D-homoserine_TMS_11	C[Si](C)(C)OCC[C@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2149.78

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
MMDBr0039017	L-Homoserine	D-homoserine	Broad specificity amino-acid racemase	Racemization	RHEA	34755880

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
Bacteria/Eubacteria	Firmicutes	1	Human feces
Bacteria	Proteobacteria	1	Human
Bacteria/Eubacteria	Proteobacteria	1	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

2006329

KEGG Compound ID

Not Available

BioCyc ID

CPD-12255

BiGG ID

Not Available

Wikipedia Link

Homoserine

METLIN ID

Not Available

PubChem Compound

2724170

PDB ID

Not Available

ChEBI ID

30654

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-homoserine (MMDBc0055867)

MOL for #<Metabolite:0x00007f9ad0401218>

3D MOL for #<Metabolite:0x00007f9ad0401218>

3D SDF for #<Metabolite:0x00007f9ad0401218>

3D-SDF for #<Metabolite:0x00007f9ad0401218>

PDB for #<Metabolite:0x00007f9ad0401218>

3D PDB for #<Metabolite:0x00007f9ad0401218>

SMILES for #<Metabolite:0x00007f9ad0401218>

INCHI for #<Metabolite:0x00007f9ad0401218>

Structure for #<Metabolite:0x00007f9ad0401218>

3D Structure for #<Metabolite:0x00007f9ad0401218>