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Showing metabocard for 4-(Methylthio)-butanonitrile (HMDB0302370)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 17:16:15 UTC
Update Date2021-09-23 17:16:15 UTC
HMDB IDHMDB0302370
Secondary Accession NumbersNone
Metabolite Identification
Common Name4-(Methylthio)-butanonitrile
Description4-(methylthio)-butanonitrile is a member of the class of compounds known as nitriles. Nitriles are compounds having the structure RC#N; thus C-substituted derivatives of hydrocyanic acid, HC#N. 4-(methylthio)-butanonitrile can be found in kohlrabi, which makes 4-(methylthio)-butanonitrile a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302370 (4-(Methylthio)-butanonitrile)


  Mrv1533004241503582D          

  7  6  0  0  0  0            999 V2000
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  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  3  0  0  0  0
M  END
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3D MOL for HMDB0302370 (4-(Methylthio)-butanonitrile)

HMDB0302370
     RDKit          3D
4-(Methylthio)-butanonitrile
 16 15  0  0  0  0  0  0  0  0999 V2000
    2.6720   -0.2716    0.0632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7767    0.5509   -1.2704 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0163    0.1060   -1.2584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5529    0.7049    0.0208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0264    0.4008    0.1631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1939   -1.0630    0.2071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3265   -2.2259    0.2308 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6675   -0.5762   -0.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1234   -1.1802    0.4367 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477    0.3874    0.9391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1421   -0.9775   -1.2538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5047    0.5088   -2.1503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3266    1.7808    0.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0256    0.1860    0.8538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6311    0.7967   -0.6790 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3737    0.8723    1.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  3  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
M  END
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3D SDF for HMDB0302370 (4-(Methylthio)-butanonitrile)


  Mrv1533004241503582D          

  7  6  0  0  0  0            999 V2000
    1.7605   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  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  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302370

> <DATABASE_NAME>
hmdb

> <SMILES>
CSCCCC#N

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NS/c1-7-5-3-2-4-6/h2-3,5H2,1H3

> <INCHI_KEY>
JPWPMBYFDCHLKL-UHFFFAOYSA-N

> <FORMULA>
C5H9NS

> <MOLECULAR_WEIGHT>
115.19

> <EXACT_MASS>
115.045570468

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
13.193572476675579

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-(methylsulfanyl)butanenitrile

> <ALOGPS_LOGP>
1.18

> <JCHEM_LOGP>
1.1814076536666667

> <ALOGPS_LOGS>
-1.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
23.79

> <JCHEM_REFRACTIVITY>
33.4592

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.14e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-(methylsulfanyl)butanenitrile

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0302370 (4-(Methylthio)-butanonitrile)

HMDB0302370
     RDKit          3D
4-(Methylthio)-butanonitrile
 16 15  0  0  0  0  0  0  0  0999 V2000
    2.6720   -0.2716    0.0632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7767    0.5509   -1.2704 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0163    0.1060   -1.2584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5529    0.7049    0.0208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0264    0.4008    0.1631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1939   -1.0630    0.2071 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3265   -2.2259    0.2308 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6675   -0.5762   -0.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1234   -1.1802    0.4367 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8477    0.3874    0.9391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1421   -0.9775   -1.2538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5047    0.5088   -2.1503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3266    1.7808    0.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0256    0.1860    0.8538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6311    0.7967   -0.6790 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3737    0.8723    1.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  3  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
M  END
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PDB for HMDB0302370 (4-(Methylthio)-butanonitrile)

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       3.286  -3.437   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       4.620  -2.667   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621  -3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955  -2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      11.288  -1.897   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0302370 (4-(Methylthio)-butanonitrile)

COMPND    HMDB0302370
HETATM    1  C1  UNL     1       2.672  -0.272   0.063  1.00  0.00           C  
HETATM    2  S1  UNL     1       1.777   0.551  -1.270  1.00  0.00           S  
HETATM    3  C2  UNL     1       0.016   0.106  -1.258  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.553   0.705   0.021  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.026   0.401   0.163  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.194  -1.063   0.207  1.00  0.00           C  
HETATM    7  N1  UNL     1      -2.327  -2.226   0.231  1.00  0.00           N  
HETATM    8  H1  UNL     1       3.667  -0.576  -0.346  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.123  -1.180   0.437  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.848   0.387   0.939  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.142  -0.978  -1.254  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.505   0.509  -2.150  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.327   1.781   0.085  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.026   0.186   0.854  1.00  0.00           H  
HETATM   15  H8  UNL     1      -2.631   0.797  -0.679  1.00  0.00           H  
HETATM   16  H9  UNL     1      -2.374   0.872   1.101  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3
CONECT    3    4   11   12
CONECT    4    5   13   14
CONECT    5    6   15   16
CONECT    6    7    7    7
END
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SMILES for HMDB0302370 (4-(Methylthio)-butanonitrile)

CSCCCC#N
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INCHI for HMDB0302370 (4-(Methylthio)-butanonitrile)

InChI=1S/C5H9NS/c1-7-5-3-2-4-6/h2-3,5H2,1H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H9NS
Average Molecular Weight115.19
Monoisotopic Molecular Weight115.045570468
IUPAC Name4-(methylsulfanyl)butanenitrile
Traditional Name4-(methylsulfanyl)butanenitrile
CAS Registry NumberNot Available
SMILES
CSCCCC#N
InChI Identifier
InChI=1S/C5H9NS/c1-7-5-3-2-4-6/h2-3,5H2,1H3
InChI KeyJPWPMBYFDCHLKL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitriles. Nitriles are compounds having the structure RC#N; thus C-substituted derivatives of hydrocyanic acid, HC#N.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassOrganic cyanides
Direct ParentNitriles
Alternative Parents
Substituents
  • Dialkylthioether
  • Sulfenyl compound
  • Thioether
  • Nitrile
  • Carbonitrile
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP1.18ALOGPS
logP1.18ChemAxon
logS-1.4ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area23.79 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity33.46 m³·mol⁻¹ChemAxon
Polarizability13.19 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
AllCCS[M+H]+125.42532859911
AllCCS[M+H-H2O]+121.27532859911
AllCCS[M+Na]+130.41132859911
AllCCS[M+NH4]+129.29432859911
AllCCS[M-H]-135.4132859911
AllCCS[M+Na-2H]-139.24632859911
AllCCS[M+HCOO]-143.48532859911
DeepCCS[M+H]+129.53930932474
DeepCCS[M-H]-127.66430932474
DeepCCS[M-2H]-163.09530932474
DeepCCS[M+Na]+137.18430932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 10V, Positive-QTOFsplash10-014i-5900000000-269e6636e8d202bbd9e82016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 20V, Positive-QTOFsplash10-0fr2-9200000000-70cb43918696df71c8672016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 40V, Positive-QTOFsplash10-0ufu-9000000000-d68e9e295d57ec18656f2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 10V, Negative-QTOFsplash10-03dj-9700000000-e7701f1127671c248fe22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 20V, Negative-QTOFsplash10-0002-9100000000-ab1f3d380983abfaa7822016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 40V, Negative-QTOFsplash10-0002-9000000000-b6ec9f4fcc739fd878b72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 10V, Positive-QTOFsplash10-014i-5900000000-02dfe6e0a2d3f973c2a52021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 20V, Positive-QTOFsplash10-052f-9000000000-57c71fe6a284d6b840772021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 40V, Positive-QTOFsplash10-03xu-9000000000-1c73698a5e59506dd5362021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 10V, Negative-QTOFsplash10-03dj-5900000000-36eef842e70ae6f9c37e2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 20V, Negative-QTOFsplash10-0002-9000000000-e1d92d2a30bee517d7542021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 4-(Methylthio)-butanonitrile 40V, Negative-QTOFsplash10-0002-9000000000-e1d92d2a30bee517d7542021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDFDB004311
KNApSAcK IDNot Available
Chemspider ID91215
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound100962
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available