MiMeDB: Showing metabocard for S-3-(hexan-1-ol)-L-cysteine (MMDBc0056299)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:22:10 UTC

Update Date

2025-10-07 16:09:43 UTC

Metabolite ID

MMDBc0056299

Metabolite Identification

Common Name

S-3-(hexan-1-ol)-L-cysteine

Description

S-3-(hexan-1-ol)-L-cysteine is a thiol-containing metabolite that belongs to the class of cysteine derivatives. Its chemical structure features a hexan-1-ol moiety linked to the sulfur atom of the cysteine side chain, making it a key precursor in the biosynthesis of volatile thiols such as 3-sulfanylhexanol (3SH), which contributes significantly to the aroma profile of certain wines. This compound is involved in various biochemical pathways, particularly in grapevine metabolism, where environmental stress can enhance its biosynthesis through the activation of glutathione S-transferases (PMID:21115666 ). It is released during fermentation processes, where yeast convert S-3-(hexan-1-ol)-L-cysteine into free thiols that impart desirable flavors to wines, particularly Sauvignon blanc (PMID:18549408 ). Additionally, S-3-(hexan-1-ol)-L-cysteine can be generated from the catabolism of S-3-(hexan-1-ol)-glutathione, further linking it to the aromatic potential of grape varieties like Merlot and Cabernet Sauvignon (PMID:12083886 ). Studies have shown that its concentration can vary in grape juices and wines, influencing the overall flavor profile (PMID:26776028 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222222D          

 16 15  0  0  1  0            999 V2000
   -0.8250    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    2.1434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    2.8579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.8579    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  5  4  1  0  0  0  0
  7  3  1  0  0  0  0
  7  4  1  0  0  0  0
  8  6  1  0  0  0  0
  9  8  1  0  0  0  0
  8 10  1  1  0  0  0
 11  5  1  0  0  0  0
 12  9  2  0  0  0  0
 13  9  1  0  0  0  0
 14  6  1  0  0  0  0
 14  7  1  0  0  0  0
 15  7  1  0  0  0  0
  8 16  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056299

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](N)(CSC([H])(CCC)CCO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H19NO3S/c1-2-3-7(4-5-11)14-6-8(10)9(12)13/h7-8,11H,2-6,10H2,1H3,(H,12,13)/t7?,8-/m0/s1

> <INCHI_KEY>
GTJBXOQYHBJVCS-MQWKRIRWSA-N

> <FORMULA>
C9H19NO3S

> <MOLECULAR_WEIGHT>
221.32

> <EXACT_MASS>
221.10856465

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
24.434170698772583

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-[(1-hydroxyhexan-3-yl)sulfanyl]propanoic acid

> <JCHEM_LOGP>
-1.8583569408657052

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.938126755752243

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.560703016702299

> <JCHEM_PKA_STRONGEST_BASIC>
9.13801394751868

> <JCHEM_POLAR_SURFACE_AREA>
83.55

> <JCHEM_REFRACTIVITY>
57.6745

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-amino-3-[(1-hydroxyhexan-3-yl)sulfanyl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -1.540   8.002   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.770   6.668   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.770   6.668   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.770   4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.850   4.001   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.540   5.335   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.390   4.001   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.160   2.667   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       6.160   5.335   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       0.770   1.334   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       7.700   2.667   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       5.390   1.334   0.000  0.00  0.00           O+0
HETATM   14  S   UNK     0       3.080   5.335   0.000  0.00  0.00           S+0
HETATM   15  H   UNK     0       0.000   5.335   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       4.620   2.667   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    7                                                       
CONECT    4    5    7                                                       
CONECT    5    4   11                                                       
CONECT    6    8   14                                                       
CONECT    7    3    4   14   15                                             
CONECT    8    6    9   10   16                                             
CONECT    9    8   12   13                                                  
CONECT   10    8                                                            
CONECT   11    5                                                            
CONECT   12    9                                                            
CONECT   13    9                                                            
CONECT   14    6    7                                                       
CONECT   15    7                                                            
CONECT   16    8                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₉NO₃S

Average Mass

221.32

Monoisotopic Mass

221.10856465

IUPAC Name

(2R)-2-amino-3-[(1-hydroxyhexan-3-yl)sulfanyl]propanoic acid

Traditional Name

(2R)-2-amino-3-[(1-hydroxyhexan-3-yl)sulfanyl]propanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H19NO3S/c1-2-3-7(4-5-11)14-6-8(10)9(12)13/h7-8,11H,2-6,10H2,1H3,(H,12,13)/t7?,8-/m0/s1

InChI Key

GTJBXOQYHBJVCS-MQWKRIRWSA-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
Alcohol
Hydrocarbon derivative
Organic oxide
Primary amine
Primary alcohol
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Amine
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.9	ChemAxon
pKa (Strongest Acidic)	2.56	ChemAxon
pKa (Strongest Basic)	9.14	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	8	ChemAxon
Refractivity	57.67 m³·mol⁻¹	ChemAxon
Polarizability	24.43 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_1_2) - 70eV, Positive	Not Available	2022-08-08	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	329.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	225.5
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	209.6
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	294.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	311.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	235.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1084.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	651.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	443.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	168.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	276.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	165.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	82.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	269.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	423.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	68.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	207.5
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1011.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	667.3

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_1	CCCC(CCO[Si](C)(C)C)SC[C@H](N)C(=O)O	standard non polar	2025-10-24	1971.17
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_2	CCCC(CCO)SC[C@H](N)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1709.33
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_3	CCCC(CCO)SC[C@H](N[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	2429.56
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_4	CCCC(CCO[Si](C)(C)C)SC[C@H](N)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1695.85
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_5	CCCC(CCO[Si](C)(C)C)SC[C@H](N[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	1875.09
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_6	CCCC(CCO)SC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1917.14
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_7	CCCC(CCO)SC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1672.78
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_8	CCCC(CCO[Si](C)(C)C)SC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	2400.55
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_9	CCCC(CCO[Si](C)(C)C)SC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1612.65
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_10	CCCC(CCO)SC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1729.24
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_11	CCCC(CCO[Si](C)(C)C)SC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1874.6
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_1	CCCC(CCO[Si](C)(C)C)SC[C@H](N)C(=O)O	standard polar	2025-10-24	1606.7
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_2	CCCC(CCO)SC[C@H](N)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1622.31
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_3	CCCC(CCO)SC[C@H](N[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2201.24
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_4	CCCC(CCO[Si](C)(C)C)SC[C@H](N)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1990.0
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_5	CCCC(CCO[Si](C)(C)C)SC[C@H](N[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	2740.21
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_6	CCCC(CCO)SC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2261.33
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_7	CCCC(CCO)SC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1136.39
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_8	CCCC(CCO[Si](C)(C)C)SC[C@H](N[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2502.78
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_9	CCCC(CCO[Si](C)(C)C)SC[C@@H](C(=O)O)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2816.11
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_10	CCCC(CCO)SC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1912.54
Gas Chromatography	S-3-(hexan-1-ol)-L-cysteine_TMS_11	CCCC(CCO[Si](C)(C)C)SC[C@@H](C(=O)O[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1588.12

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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

57559164

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53251240

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-3-(hexan-1-ol)-L-cysteine (MMDBc0056299)

MOL for #<Metabolite:0x00005643230b68c0>

3D MOL for #<Metabolite:0x00005643230b68c0>

3D SDF for #<Metabolite:0x00005643230b68c0>

3D-SDF for #<Metabolite:0x00005643230b68c0>

PDB for #<Metabolite:0x00005643230b68c0>

3D PDB for #<Metabolite:0x00005643230b68c0>

SMILES for #<Metabolite:0x00005643230b68c0>

INCHI for #<Metabolite:0x00005643230b68c0>

Structure for #<Metabolite:0x00005643230b68c0>

3D Structure for #<Metabolite:0x00005643230b68c0>