MiMeDB: Showing metabocard for 2-Methylserine (MMDBc0000718)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:53:27 UTC

Update Date

2025-10-07 16:04:13 UTC

Metabolite ID

MMDBc0000718

Metabolite Identification

Common Name

2-Methylserine

Description

2-Methylserine is a non-proteinogenic amino acid classified as a derivative of serine. Its chemical structure features a methyl group attached to the second carbon of the serine backbone, which influences its biochemical properties and interactions. In metabolic pathways, 2-methylserine has been implicated in various physiological processes, including its association with tuberculosis (TB) progression; studies indicate that an increase in metabolites like 2-methylserine correlates with inhibited TB progression (PMID:40515933 ). Additionally, it has been linked to intervertebral disc degeneration (IVDD), where it, along with other metabolites, showed significant associations in a two-step Mendelian randomization analysis (PMID:40211528 ). Furthermore, 2-methylserine's conformational behavior has been explored in peptide studies, demonstrating its potential to induce helical structures in specific host-guest peptide configurations, as analyzed through circular dichroism and infrared spectroscopy (PMID:3145251 ). This highlights its relevance not only in metabolic contexts but also in structural biology, where it may influence peptide conformation and stability.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2-Ammonio-3-hydroxy-2-methylpropanoate	ChEBI
2-Methylserine	ChEBI
2-Ammonio-3-hydroxy-2-methylpropanoic acid	Generator
2-amino-2-Methyl-3-hydroxypropanoic acid	ChEBI
2-amino-2-Methyl-3-hydroxypropanoate	Generator
alpha-Methylserine	MeSH
2-Methylserine, (DL-ser)-isomer	MeSH

Molecular Formula

C₄H₉NO₃

Average Mass

119.1192

Monoisotopic Mass

119.058243159

IUPAC Name

2-amino-3-hydroxy-2-methylpropanoic acid

Traditional Name

2-methylserine

CAS Registry Number

Not Available

SMILES

CC(N)(CO)C(O)=O

InChI Identifier

InChI=1S/C4H9NO3/c1-4(5,2-6)3(7)8/h6H,2,5H2,1H3,(H,7,8)

InChI Key

CDUUKBXTEOFITR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids

Alternative Parents

Substituents

Alpha-amino acid
Beta-hydroxy acid
Hydroxy acid
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Alcohol
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Primary aliphatic amine
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Amine
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

non-proteinogenic alpha-amino acid (CHEBI:17799 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	433 g/L	ALOGPS
logP	-3	ALOGPS
logP	-3.5	ChemAxon
logS	0.56	ALOGPS
pKa (Strongest Acidic)	2.17	ChemAxon
pKa (Strongest Basic)	9.18	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	2	ChemAxon
Refractivity	26.75 m³·mol⁻¹	ChemAxon
Polarizability	11.22 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 (2 TMS)	splash10-01qa-1900000000-b321b9d88384fdb94c54	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-02ai-1960000000-278dd3cf6328d3c74b6e	2014-06-16	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
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	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)	2025-10-23	460.4
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	370.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	39.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	222.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	291.2
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	335.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	486.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	798.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	805.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	199.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	483.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	210.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	41.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	372.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	653.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	75.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	290.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (void)	2025-10-23	659.9
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	583.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	2-Methylserine_TMS_1	CC(N)(CO[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	1717.4
Gas Chromatography	2-Methylserine_TMS_2	CC(N)(CO)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1875.64
Gas Chromatography	2-Methylserine_TMS_3	CC(CO)(N[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	2134.24
Gas Chromatography	2-Methylserine_TMS_4	CC(N)(CO[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1844.62
Gas Chromatography	2-Methylserine_TMS_5	CC(CO[Si](C)(C)C)(N[Si](C)(C)C)C(=O)O	standard non polar	2025-10-23	1984.88
Gas Chromatography	2-Methylserine_TMS_6	CC(CO)(N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	1585.84
Gas Chromatography	2-Methylserine_TMS_7	CC(CO)(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1884.63
Gas Chromatography	2-Methylserine_TMS_8	CC(CO[Si](C)(C)C)(N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-23	2261.88
Gas Chromatography	2-Methylserine_TMS_9	CC(CO[Si](C)(C)C)(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	2137.78
Gas Chromatography	2-Methylserine_TMS_10	CC(CO)(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1594.58
Gas Chromatography	2-Methylserine_TMS_11	CC(CO[Si](C)(C)C)(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-23	1573.05
Gas Chromatography	2-Methylserine_TMS_1	CC(N)(CO[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	2335.67
Gas Chromatography	2-Methylserine_TMS_2	CC(N)(CO)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1925.62
Gas Chromatography	2-Methylserine_TMS_3	CC(CO)(N[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	2140.78
Gas Chromatography	2-Methylserine_TMS_4	CC(N)(CO[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2085.01
Gas Chromatography	2-Methylserine_TMS_5	CC(CO[Si](C)(C)C)(N[Si](C)(C)C)C(=O)O	standard polar	2025-10-23	1732.4
Gas Chromatography	2-Methylserine_TMS_6	CC(CO)(N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	2035.9
Gas Chromatography	2-Methylserine_TMS_7	CC(CO)(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2403.21
Gas Chromatography	2-Methylserine_TMS_8	CC(CO[Si](C)(C)C)(N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-23	1495.84
Gas Chromatography	2-Methylserine_TMS_9	CC(CO[Si](C)(C)C)(C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	1749.06
Gas Chromatography	2-Methylserine_TMS_10	CC(CO)(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	1963.82
Gas Chromatography	2-Methylserine_TMS_11	CC(CO[Si](C)(C)C)(C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-23	2120.93

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	Bacteroidetes	2	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria/Eubacteria	Firmicutes	2	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen

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

HMDB0240310

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CPD-390

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

94309

PDB ID

Not Available

ChEBI ID

58275

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Showing metabocard for 2-Methylserine (MMDBc0000718)

MOL for #<Metabolite:0x00007f9aceb8e7f8>

3D MOL for #<Metabolite:0x00007f9aceb8e7f8>

3D SDF for #<Metabolite:0x00007f9aceb8e7f8>

3D-SDF for #<Metabolite:0x00007f9aceb8e7f8>

PDB for #<Metabolite:0x00007f9aceb8e7f8>

3D PDB for #<Metabolite:0x00007f9aceb8e7f8>

SMILES for #<Metabolite:0x00007f9aceb8e7f8>

INCHI for #<Metabolite:0x00007f9aceb8e7f8>

Structure for #<Metabolite:0x00007f9aceb8e7f8>

3D Structure for #<Metabolite:0x00007f9aceb8e7f8>