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Showing metabocard for Isopentyl mercaptan (HMDB0033902)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:40:39 UTC
Update Date2023-02-21 17:23:44 UTC
HMDB IDHMDB0033902
Secondary Accession Numbers
  • HMDB33902
Metabolite Identification
Common NameIsopentyl mercaptan
DescriptionIsopentyl mercaptan belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain. Isopentyl mercaptan is a glue and onion tasting compound. Isopentyl mercaptan has been detected, but not quantified in, alcoholic beverages. This could make isopentyl mercaptan a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Isopentyl mercaptan.
Structure
Data?1677000224
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033902 (Isopentyl mercaptan)


  Mrv0541 05061307262D          

  6  5  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    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
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
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3D MOL for HMDB0033902 (Isopentyl mercaptan)

HMDB0033902
     RDKit          3D
Isopentyl mercaptan
 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.0826    1.2824    0.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7073   -0.1542   -0.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8481   -1.0314    0.2368 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5760   -0.5173    0.5697 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7122    0.4001    0.1248 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2121   -0.0648    1.0296 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8336    1.4728    1.1966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1673    1.4725    0.0244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4678    1.9996   -0.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5768   -0.2441   -1.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0687   -1.8515   -0.4567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7995   -0.4667    0.3853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6066   -1.4552    1.2478 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8467   -1.5704    0.4177 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4094   -0.3319    1.6503 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4709    1.4618    0.3295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8714    0.3297   -0.9734 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0596   -0.7316    0.1250 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
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3D SDF for HMDB0033902 (Isopentyl mercaptan)


  Mrv0541 05061307262D          

  6  5  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    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
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033902

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)CCS

> <INCHI_IDENTIFIER>
InChI=1S/C5H12S/c1-5(2)3-4-6/h5-6H,3-4H2,1-2H3

> <INCHI_KEY>
GIJGXNFNUUFEGH-UHFFFAOYSA-N

> <FORMULA>
C5H12S

> <MOLECULAR_WEIGHT>
104.214

> <EXACT_MASS>
104.065971074

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
13.103151957488802

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylbutane-1-thiol

> <ALOGPS_LOGP>
2.85

> <JCHEM_LOGP>
2.3437104383333334

> <ALOGPS_LOGS>
-2.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.198550804630978

> <JCHEM_PKA_STRONGEST_BASIC>
-9.55991162800997

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
32.7121

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.17e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isoamylthiol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0033902 (Isopentyl mercaptan)

HMDB0033902
     RDKit          3D
Isopentyl mercaptan
 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.0826    1.2824    0.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7073   -0.1542   -0.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8481   -1.0314    0.2368 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5760   -0.5173    0.5697 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7122    0.4001    0.1248 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2121   -0.0648    1.0296 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8336    1.4728    1.1966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1673    1.4725    0.0244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4678    1.9996   -0.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5768   -0.2441   -1.2592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0687   -1.8515   -0.4567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7995   -0.4667    0.3853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6066   -1.4552    1.2478 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8467   -1.5704    0.4177 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4094   -0.3319    1.6503 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4709    1.4618    0.3295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8714    0.3297   -0.9734 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0596   -0.7316    0.1250 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
M  END
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PDB for HMDB0033902 (Isopentyl mercaptan)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    5                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    1    2    3                                                  
CONECT    6    4                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0033902 (Isopentyl mercaptan)

COMPND    HMDB0033902
HETATM    1  C1  UNL     1      -1.083   1.282   0.127  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.707  -0.154  -0.174  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.848  -1.031   0.237  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.576  -0.517   0.570  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.712   0.400   0.125  1.00  0.00           C  
HETATM    6  S1  UNL     1       3.212  -0.065   1.030  1.00  0.00           S  
HETATM    7  H1  UNL     1      -0.834   1.473   1.197  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.167   1.472   0.024  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.468   2.000  -0.458  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.577  -0.244  -1.259  1.00  0.00           H  
HETATM   11  H5  UNL     1      -2.069  -1.851  -0.457  1.00  0.00           H  
HETATM   12  H6  UNL     1      -2.800  -0.467   0.385  1.00  0.00           H  
HETATM   13  H7  UNL     1      -1.607  -1.455   1.248  1.00  0.00           H  
HETATM   14  H8  UNL     1       0.847  -1.570   0.418  1.00  0.00           H  
HETATM   15  H9  UNL     1       0.409  -0.332   1.650  1.00  0.00           H  
HETATM   16  H10 UNL     1       1.471   1.462   0.330  1.00  0.00           H  
HETATM   17  H11 UNL     1       1.871   0.330  -0.973  1.00  0.00           H  
HETATM   18  H12 UNL     1       4.060  -0.732   0.125  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    4   10
CONECT    3   11   12   13
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6   18
END
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SMILES for HMDB0033902 (Isopentyl mercaptan)

CC(C)CCS
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INCHI for HMDB0033902 (Isopentyl mercaptan)

InChI=1S/C5H12S/c1-5(2)3-4-6/h5-6H,3-4H2,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-mercapto-3-MethylbutaneHMDB
2-Methyl-4-butanethiolHMDB
3-Methyl-1-butanethiolHMDB
3-Methyl-1-butylthiolHMDB
3-Methylbutane-1-thiolHMDB
3-MethylbutanethiolHMDB
FEMA 3858HMDB
Isoamyl mercaptanHMDB
Isoamyl sulfhydrateHMDB
Isoamyl thioalcoholHMDB
IsoamylthiolHMDB
IsopentanethiolHMDB
Thioisoamyl alcoholHMDB
Chemical FormulaC5H12S
Average Molecular Weight104.214
Monoisotopic Molecular Weight104.065971074
IUPAC Name3-methylbutane-1-thiol
Traditional Nameisoamylthiol
CAS Registry Number541-31-1
SMILES
CC(C)CCS
InChI Identifier
InChI=1S/C5H12S/c1-5(2)3-4-6/h5-6H,3-4H2,1-2H3
InChI KeyGIJGXNFNUUFEGH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkylthiols. These are organic compounds containing the thiol functional group linked to an alkyl chain.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassThiols
Sub ClassAlkylthiols
Direct ParentAlkylthiols
Alternative Parents
Substituents
  • Alkylthiol
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point119.00 to 120.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility599.2 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.670The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.62 g/LALOGPS
logP2.85ALOGPS
logP2.34ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)10.2ChemAxon
pKa (Strongest Basic)-9.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity32.71 m³·mol⁻¹ChemAxon
Polarizability13.1 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+120.46831661259
DarkChem[M-H]-114.52931661259
DeepCCS[M+H]+131.11530932474
DeepCCS[M-H]-128.93130932474
DeepCCS[M-2H]-164.54630932474
DeepCCS[M+Na]+139.12530932474
AllCCS[M+H]+123.632859911
AllCCS[M+H-H2O]+119.432859911
AllCCS[M+NH4]+127.632859911
AllCCS[M+Na]+128.832859911
AllCCS[M-H]-137.432859911
AllCCS[M+Na-2H]-142.232859911
AllCCS[M+HCOO]-147.432859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.3.84 minutes32390414
Predicted by Siyang on May 30, 202217.886 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.82 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid97.1 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2366.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid727.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid270.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid497.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid325.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid700.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid778.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)623.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1346.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid460.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1523.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid507.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid433.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate728.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA640.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water124.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Isopentyl mercaptanCC(C)CCS983.8Standard polar33892256
Isopentyl mercaptanCC(C)CCS776.7Standard non polar33892256
Isopentyl mercaptanCC(C)CCS807.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Isopentyl mercaptan,1TMS,isomer #1CC(C)CCS[Si](C)(C)C1031.5Semi standard non polar33892256
Isopentyl mercaptan,1TMS,isomer #1CC(C)CCS[Si](C)(C)C1006.4Standard non polar33892256
Isopentyl mercaptan,1TBDMS,isomer #1CC(C)CCS[Si](C)(C)C(C)(C)C1246.7Semi standard non polar33892256
Isopentyl mercaptan,1TBDMS,isomer #1CC(C)CCS[Si](C)(C)C(C)(C)C1222.5Standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB012097
KNApSAcK IDNot Available
Chemspider ID10462
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10925
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1108121
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .