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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 16:01:15 UTC

Update Date

2021-09-23 16:01:16 UTC

HMDB ID

HMDB0302211

Secondary Accession Numbers

None

Metabolite Identification

Common Name

S-N-Methylcysteine

Description

S-n-methylcysteine, also known as (2r)-2-amino-3-(methylsulfanyl)propanoic acid or 3-(methylthio)-L-alanine, is a member of the class of compounds known as L-cysteine-s-conjugates. L-cysteine-s-conjugates are compounds containing L-cysteine where the thio-group is conjugated. S-n-methylcysteine is soluble (in water) and a moderately acidic compound (based on its pKa). S-n-methylcysteine can be found in soft-necked garlic, which makes S-n-methylcysteine a potential biomarker for the consumption of this food product. S-n-methylcysteine can be found primarily in blood and urine.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View Stereo Labels

Synonyms

Value	Source
(2R)-2-Amino-3-(methylsulfanyl)propanoic acid	ChEBI
(R)-2-Amino-3-(methylthio)propanoic acid	ChEBI
3-(Methylthio)-L-alanine	ChEBI
L-Methylcysteine	ChEBI
S-Methyl-L-cysteine	ChEBI
(2R)-2-Amino-3-(methylsulfanyl)propanoate	Generator
(2R)-2-Amino-3-(methylsulphanyl)propanoate	Generator
(2R)-2-Amino-3-(methylsulphanyl)propanoic acid	Generator
(R)-2-Amino-3-(methylthio)propanoate	Generator
3-(methylthio)-L-(8CI)alanine	HMDB
Acm-thiopropionate	HMDB
Acm-thiopropionic acid	HMDB
L-Aspartic acid dimethyl ester	HMDB
S-Acetamidomethyl-deamino-cysteine	HMDB
S-Methyl-(9ci)-L-cysteine	HMDB
S-Methyl-cysteine	HMDB
S-Methyl-DL-cysteine	HMDB
S-Methylcysteine	HMDB, MeSH
S-11C-Methyl-L-cysteine	MeSH, HMDB
S-Methylcysteine, (DL-cys)-isomer	MeSH, HMDB
S-Methylcysteine, hydrochloride, (L-cys)-isomer	MeSH, HMDB
S-Methylcysteine, (L-cys)-isomer	MeSH, HMDB

Chemical Formula

C₄H₉NO₂S

Average Molecular Weight

135.185

Monoisotopic Molecular Weight

135.035399227

IUPAC Name

(2R)-2-amino-3-(methylsulfanyl)propanoic acid

Traditional Name

S-methylcysteine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C4H9NO2S/c1-8-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m0/s1

InChI Key

IDIDJDIHTAOVLG-VKHMYHEASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-cysteine-s-conjugates. L-cysteine-S-conjugates are compounds containing L-cysteine where the thio-group is conjugated.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-cysteine-S-conjugates

Alternative Parents

Substituents

L-cysteine-s-conjugate
Alpha-amino acid
L-alpha-amino acid
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Thioether
Sulfenyl compound
Dialkylthioether
Carbonyl group
Amine
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Primary aliphatic amine
Organic oxygen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

S-alkyl-L-cysteine (CHEBI:45658 )

Ontology

Not Available

Exogenous (HMDB: HMDB0302211)

Food

Herb and spice

Herb

Garlic (HMDB: HMDB0302211)
Soft-necked garlic (FooDB: FOOD00850)

Vegetable

Onion-family vegetable

Onion family vegetables (HMDB: HMDB0302211)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.2	ALOGPS
logP	-2.4	ChemAxon
logS	-0.31	ALOGPS
pKa (Strongest Acidic)	2.44	ChemAxon
pKa (Strongest Basic)	9.15	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	32.87 m³·mol⁻¹	ChemAxon
Polarizability	13.56 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
AllCCS	[M+H]+	131.073	32859911
AllCCS	[M+H-H2O]+	127.072	32859911
AllCCS	[M+Na]+	135.874	32859911
AllCCS	[M+NH4]+	134.8	32859911
AllCCS	[M-H]-	132.057	32859911
AllCCS	[M+Na-2H]-	135.358	32859911
AllCCS	[M+HCOO]-	139.012	32859911
DeepCCS	[M+H]+	123.201	30932474
DeepCCS	[M-H]-	119.63	30932474
DeepCCS	[M-2H]-	156.716	30932474
DeepCCS	[M+Na]+	132.04	30932474

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	9.8452 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	7.54 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	671.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	360.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	49.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	225.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	73.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	274.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	273.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	786.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	666.4 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	52.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	759.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	206.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	236.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	591.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	394.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	287.4 seconds	40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
S-N-Methylcysteine,2TMS,isomer #1	CSC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	1412.7	Semi standard non polar	33892256
S-N-Methylcysteine,2TMS,isomer #1	CSC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	1384.5	Standard non polar	33892256
S-N-Methylcysteine,2TMS,isomer #1	CSC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	1733.0	Standard polar	33892256
S-N-Methylcysteine,2TMS,isomer #2	CSC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1555.3	Semi standard non polar	33892256
S-N-Methylcysteine,2TMS,isomer #2	CSC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1468.1	Standard non polar	33892256
S-N-Methylcysteine,2TMS,isomer #2	CSC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	1866.4	Standard polar	33892256
S-N-Methylcysteine,3TMS,isomer #1	CSC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1570.9	Semi standard non polar	33892256
S-N-Methylcysteine,3TMS,isomer #1	CSC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1532.6	Standard non polar	33892256
S-N-Methylcysteine,3TMS,isomer #1	CSC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	1610.7	Standard polar	33892256
S-N-Methylcysteine,2TBDMS,isomer #1	CSC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1881.6	Semi standard non polar	33892256
S-N-Methylcysteine,2TBDMS,isomer #1	CSC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1819.3	Standard non polar	33892256
S-N-Methylcysteine,2TBDMS,isomer #1	CSC[C@H](N[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1939.1	Standard polar	33892256
S-N-Methylcysteine,2TBDMS,isomer #2	CSC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1990.8	Semi standard non polar	33892256
S-N-Methylcysteine,2TBDMS,isomer #2	CSC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	1907.8	Standard non polar	33892256
S-N-Methylcysteine,2TBDMS,isomer #2	CSC[C@@H](C(=O)O)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2006.7	Standard polar	33892256
S-N-Methylcysteine,3TBDMS,isomer #1	CSC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2255.4	Semi standard non polar	33892256
S-N-Methylcysteine,3TBDMS,isomer #1	CSC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2160.7	Standard non polar	33892256
S-N-Methylcysteine,3TBDMS,isomer #1	CSC[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2001.3	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - S-N-Methylcysteine GC-MS (1 TMS)	splash10-0006-9500000000-daa44ef1254b2abffd37	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - S-N-Methylcysteine GC-MS (2 TMS)	splash10-02t9-1950000000-7418765e9cc42b0155e4	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - S-N-Methylcysteine EI-B (Non-derivatized)	splash10-03fv-9000000000-d790345dc4143a2c43ef	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - S-N-Methylcysteine GC-MS (Non-derivatized)	splash10-0006-9500000000-daa44ef1254b2abffd37	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - S-N-Methylcysteine GC-MS (Non-derivatized)	splash10-02t9-1950000000-7418765e9cc42b0155e4	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - S-N-Methylcysteine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9000000000-72d010b2583bd53b7e08	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - S-N-Methylcysteine GC-MS (1 TMS) - 70eV, Positive	splash10-006y-9400000000-3b5fc90a341033d6e213	2017-10-06	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - S-N-Methylcysteine Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-014i-1900000000-4a373aa1d088e914bead	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - S-N-Methylcysteine Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-00b9-9000000000-04c165848579841841db	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - S-N-Methylcysteine Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-00fr-9000000000-1b77045ef8e2cb3b10e8	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - S-N-Methylcysteine EI-B (HITACHI M-80) , Positive-QTOF	splash10-03fv-9000000000-9377aea80fe674b0a8de	2012-08-31	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 10V, Positive-QTOF	splash10-000f-9700000000-8f3d25ac52279c092856	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 20V, Positive-QTOF	splash10-0006-9200000000-b405850a71df669cec12	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 40V, Positive-QTOF	splash10-006x-9000000000-ace8060e79e2568e8fd6	2017-07-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 10V, Negative-QTOF	splash10-0002-9200000000-0100ccbfcee39a28f73d	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 20V, Negative-QTOF	splash10-000b-9000000000-77f7473e8f64b00cba29	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 40V, Negative-QTOF	splash10-0002-9000000000-5f83877d00d54983d86c	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 10V, Positive-QTOF	splash10-01bc-7900000000-15e4c05adb56715c93d8	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 20V, Positive-QTOF	splash10-00dm-9000000000-5a8e96324e324aab8703	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 40V, Positive-QTOF	splash10-0002-9000000000-c69e8c7f456c0f6fa275	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 10V, Negative-QTOF	splash10-0002-9000000000-e1d92d2a30bee517d754	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 20V, Negative-QTOF	splash10-0002-9000000000-e1d92d2a30bee517d754	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - S-N-Methylcysteine 40V, Negative-QTOF	splash10-0002-9000000000-e1d92d2a30bee517d754	2021-10-21	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB02216

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB003689

KNApSAcK ID

C00000747

Chemspider ID

22826

KEGG Compound ID

Not Available

BioCyc ID

S-METHYL-L-CYSTEINE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

45658

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1281351

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for S-N-Methylcysteine (HMDB0302211)

MOL for HMDB0302211 (S-N-Methylcysteine)

3D MOL for HMDB0302211 (S-N-Methylcysteine)

3D SDF for HMDB0302211 (S-N-Methylcysteine)

3D-SDF for HMDB0302211 (S-N-Methylcysteine)

PDB for HMDB0302211 (S-N-Methylcysteine)

3D PDB for HMDB0302211 (S-N-Methylcysteine)

SMILES for HMDB0302211 (S-N-Methylcysteine)

INCHI for HMDB0302211 (S-N-Methylcysteine)

Structure for HMDB0302211 (S-N-Methylcysteine)

3D Structure for HMDB0302211 (S-N-Methylcysteine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra