MiMeDB: Showing metabocard for S-benzyl-L-cysteine (MMDBc0054659)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:23:03 UTC

Update Date

2025-10-07 16:08:37 UTC

Metabolite ID

MMDBc0054659

Metabolite Identification

Common Name

S-benzyl-L-cysteine

Description

S-benzyl-L-cysteine is a sulfur-containing amino acid derivative classified within the chemical class of cysteine analogs. Its chemical structure features a benzyl group attached to the sulfur atom of the cysteine backbone, which influences its reactivity and interactions in various biochemical pathways. S-benzyl-L-cysteine has been shown to play a role in the inhibition of sulfur assimilation, impacting growth and photosynthesis in maize plants, as documented in PMID:39362125 . Additionally, it is involved in the synthesis of polypeptides, demonstrating mechanical reinforcement properties in materials science, particularly in poly(S-benzyl-L-cysteine) formulations that exhibit stability at elevated temperatures (PMID:40262034 ). The compound has also been utilized in advanced solar cell technologies, where it serves as a passivation agent to improve interface stability in perovskite solar cells (PMID:40177884 ). Furthermore, S-benzyl-L-cysteine has been explored in the context of cyclic dipeptides, revealing its potential in self-assembly and gelation processes (PMID:38853148 ). Overall, S-benzyl-L-cysteine emerges as a versatile compound with applications spanning both biological and material sciences.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231217442D          

 14 14  0  0  1  0            999 V2000
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054659

> <DATABASE_NAME>
MIME

> <SMILES>
N[C@@H](CSCC1=CC=CC=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13NO2S/c11-9(10(12)13)7-14-6-8-4-2-1-3-5-8/h1-5,9H,6-7,11H2,(H,12,13)/t9-/m0/s1

> <INCHI_KEY>
GHBAYRBVXCRIHT-VIFPVBQESA-N

> <FORMULA>
C10H13NO2S

> <MOLECULAR_WEIGHT>
211.281

> <EXACT_MASS>
211.066699355

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
22.673928516700407

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-(benzylsulfanyl)propanoic acid

> <ALOGPS_LOGP>
-0.84

> <JCHEM_LOGP>
-0.7841061019482994

> <ALOGPS_LOGS>
-2.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.4173224216262876

> <JCHEM_PKA_STRONGEST_BASIC>
9.136546476674273

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
57.536400000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
benzylcysteine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    2   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

Synonyms

Value	Source
S-Benzylcysteine, 2-13C-labeled	MeSH
S-Benzylcysteine	MeSH

Molecular Formula

C₁₀H₁₃NO₂S

Average Mass

211.281

Monoisotopic Mass

211.066699355

IUPAC Name

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

Traditional Name

benzylcysteine

CAS Registry Number

Not Available

SMILES

N[C@@H](CSCC1=CC=CC=C1)C(O)=O

InChI Identifier

InChI=1S/C10H13NO2S/c11-9(10(12)13)7-14-6-8-4-2-1-3-5-8/h1-5,9H,6-7,11H2,(H,12,13)/t9-/m0/s1

InChI Key

GHBAYRBVXCRIHT-VIFPVBQESA-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
Monocyclic benzene moiety
Benzenoid
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Thioether
Sulfenyl compound
Dialkylthioether
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Amine
Primary aliphatic amine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

S-hydrocarbyl-L-cysteine (CHEBI:41085 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.07 g/L	ALOGPS
logP	-0.84	ALOGPS
logP	-0.78	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	2.42	ChemAxon
pKa (Strongest Basic)	9.14	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	5	ChemAxon
Refractivity	57.54 m³·mol⁻¹	ChemAxon
Polarizability	22.67 Å³	ChemAxon
Number of Rings	1	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 (Non-derivatized) - 70eV, Positive	splash10-0006-9400000000-d382200f85f43d31a2e6	2017-08-28	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0296-7920000000-922d2911711fc139d997	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-006x-9800000000-152b3465345cf554b631	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9200000000-983a99c19fb9dc632a7c	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-4930000000-1b9061bb42aca83f8f11	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-5900000000-34e760c4850aad6b77db	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0079-9200000000-c03518c497896e758b18	2017-07-26	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	374.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	188.5
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	294.9
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	411.6
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	299.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	302.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1084.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	639.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	461.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	176.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	314.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	184.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	101.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	125.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	408.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	84.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	255.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	933.3
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	762.6

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	S-benzyl-L-cysteine_TMS_1	C[Si](C)(C)OC(=O)[C@@H](N)CSCC1=CC=CC=C1	standard non polar	2025-10-24	1869.24
Gas Chromatography	S-benzyl-L-cysteine_TMS_2	C[Si](C)(C)N[C@@H](CSCC1=CC=CC=C1)C(=O)O	standard non polar	2025-10-24	1894.15
Gas Chromatography	S-benzyl-L-cysteine_TMS_3	C[Si](C)(C)N[C@@H](CSCC1=CC=CC=C1)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2127.58
Gas Chromatography	S-benzyl-L-cysteine_TMS_4	C[Si](C)(C)N([C@@H](CSCC1=CC=CC=C1)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	1759.98
Gas Chromatography	S-benzyl-L-cysteine_TMS_5	C[Si](C)(C)OC(=O)[C@H](CSCC1=CC=CC=C1)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1913.09
Gas Chromatography	S-benzyl-L-cysteine_TMS_1	C[Si](C)(C)OC(=O)[C@@H](N)CSCC1=CC=CC=C1	standard polar	2025-10-24	2274.59
Gas Chromatography	S-benzyl-L-cysteine_TMS_2	C[Si](C)(C)N[C@@H](CSCC1=CC=CC=C1)C(=O)O	standard polar	2025-10-24	1927.21
Gas Chromatography	S-benzyl-L-cysteine_TMS_3	C[Si](C)(C)N[C@@H](CSCC1=CC=CC=C1)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1972.73
Gas Chromatography	S-benzyl-L-cysteine_TMS_4	C[Si](C)(C)N([C@@H](CSCC1=CC=CC=C1)C(=O)O)[Si](C)(C)C	standard polar	2025-10-24	2029.14
Gas Chromatography	S-benzyl-L-cysteine_TMS_5	C[Si](C)(C)OC(=O)[C@H](CSCC1=CC=CC=C1)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1979.74

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	Actinobacteria	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

DB04531

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

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

193613

PDB ID

Not Available

ChEBI ID

Not Available

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 S-benzyl-L-cysteine (MMDBc0054659)

MOL for #<Metabolite:0x0000564322fc74f0>

3D MOL for #<Metabolite:0x0000564322fc74f0>

3D SDF for #<Metabolite:0x0000564322fc74f0>

3D-SDF for #<Metabolite:0x0000564322fc74f0>

PDB for #<Metabolite:0x0000564322fc74f0>

3D PDB for #<Metabolite:0x0000564322fc74f0>

SMILES for #<Metabolite:0x0000564322fc74f0>

INCHI for #<Metabolite:0x0000564322fc74f0>

Structure for #<Metabolite:0x0000564322fc74f0>

3D Structure for #<Metabolite:0x0000564322fc74f0>