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Showing metabocard for 1-Isothiocyanatopentane (HMDB0038433)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 23:45:01 UTC
Update Date2023-02-21 17:26:33 UTC
HMDB IDHMDB0038433
Secondary Accession Numbers
  • HMDB38433
Metabolite Identification
Common Name1-Isothiocyanatopentane
Description1-Isothiocyanatopentane belongs to the class of organic compounds known as isothiocyanates. These are organic compounds containing the isothiocyanate group, an isocyanate analogue with the general formula RN=C=S. 1-Isothiocyanatopentane is a green tasting compound. 1-Isothiocyanatopentane has been detected, but not quantified in, brassicas. This could make 1-isothiocyanatopentane a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1-Isothiocyanatopentane.
Structure
Data?1677000393
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0038433 (1-Isothiocyanatopentane)


  Mrv0541 05061310272D          

  8  7  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    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
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    0.3020    0.0000 S   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
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  2  0  0  0  0
M  END
Download

3D MOL for HMDB0038433 (1-Isothiocyanatopentane)

HMDB0038433
     RDKit          3D
1-Isothiocyanatopentane
 19 18  0  0  0  0  0  0  0  0999 V2000
   -1.8740    1.3985   -0.3984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7690    0.1673    0.4558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7844   -0.8110   -0.1634 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5948   -0.2007   -0.2875 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4992   -1.2333   -0.9065 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8551   -0.7474   -1.0713 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1866    0.2620   -0.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9368    1.5373    0.2141 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6990    2.0182    0.0287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9118    1.9698   -0.3675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1295    1.1699   -1.4411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7529   -0.3370    0.4618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4960    0.4380    1.4783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6893   -1.7203    0.4635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1366   -1.0503   -1.1882 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0172    0.0682    0.6936 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5803    0.6919   -0.9403 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1109   -1.4454   -1.9184 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4614   -2.1756   -0.3118 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  2  0
  7  8  2  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
M  END
Download

3D SDF for HMDB0038433 (1-Isothiocyanatopentane)


  Mrv0541 05061310272D          

  8  7  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    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
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    0.3020    0.0000 S   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
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0038433

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCN=C=S

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NS/c1-2-3-4-5-7-6-8/h2-5H2,1H3

> <INCHI_KEY>
SGHJUJBYMSVAJY-UHFFFAOYSA-N

> <FORMULA>
C6H11NS

> <MOLECULAR_WEIGHT>
129.223

> <EXACT_MASS>
129.061220047

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
15.452990834155603

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-isothiocyanatopentane

> <ALOGPS_LOGP>
3.43

> <JCHEM_LOGP>
2.838117733666667

> <ALOGPS_LOGS>
-3.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.768786878059903

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
39.8037

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-isothiocyanatopentane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0038433 (1-Isothiocyanatopentane)

HMDB0038433
     RDKit          3D
1-Isothiocyanatopentane
 19 18  0  0  0  0  0  0  0  0999 V2000
   -1.8740    1.3985   -0.3984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7690    0.1673    0.4558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7844   -0.8110   -0.1634 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5948   -0.2007   -0.2875 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4992   -1.2333   -0.9065 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8551   -0.7474   -1.0713 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1866    0.2620   -0.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9368    1.5373    0.2141 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6990    2.0182    0.0287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9118    1.9698   -0.3675 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1295    1.1699   -1.4411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7529   -0.3370    0.4618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4960    0.4380    1.4783 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6893   -1.7203    0.4635 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1366   -1.0503   -1.1882 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0172    0.0682    0.6936 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5803    0.6919   -0.9403 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1109   -1.4454   -1.9184 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4614   -2.1756   -0.3118 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  2  0
  7  8  2  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
M  END
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PDB for HMDB0038433 (1-Isothiocyanatopentane)

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      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   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       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.645   1.334   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       6.311   2.104   0.000  0.00  0.00           N+0
HETATM    8  S   UNK     0       8.978   0.564   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    7                                                       
CONECT    6    7    8                                                       
CONECT    7    5    6                                                       
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0038433 (1-Isothiocyanatopentane)

COMPND    HMDB0038433
HETATM    1  C1  UNL     1      -1.874   1.398  -0.398  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.769   0.167   0.456  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.784  -0.811  -0.163  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.595  -0.201  -0.287  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.499  -1.233  -0.906  1.00  0.00           C  
HETATM    6  N1  UNL     1       2.855  -0.747  -1.071  1.00  0.00           N  
HETATM    7  C6  UNL     1       3.187   0.262  -0.372  1.00  0.00           C  
HETATM    8  S1  UNL     1       3.937   1.537   0.214  1.00  0.00           S  
HETATM    9  H1  UNL     1      -2.699   2.018   0.029  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.912   1.970  -0.368  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.129   1.170  -1.441  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.753  -0.337   0.462  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.496   0.438   1.478  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.689  -1.720   0.464  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.137  -1.050  -1.188  1.00  0.00           H  
HETATM   16  H8  UNL     1       1.017   0.068   0.694  1.00  0.00           H  
HETATM   17  H9  UNL     1       0.580   0.692  -0.940  1.00  0.00           H  
HETATM   18  H10 UNL     1       1.111  -1.445  -1.918  1.00  0.00           H  
HETATM   19  H11 UNL     1       1.461  -2.176  -0.312  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3   12   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7    7
CONECT    7    8    8
END
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SMILES for HMDB0038433 (1-Isothiocyanatopentane)

CCCCCN=C=S
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INCHI for HMDB0038433 (1-Isothiocyanatopentane)

InChI=1S/C6H11NS/c1-2-3-4-5-7-6-8/h2-5H2,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-isothiocyanato-PentaneHMDB
N-Amyl isothiocyanateHMDB
N-Pentyl isothiocyanateHMDB
Pentyl isothiocyanateHMDB
Chemical FormulaC6H11NS
Average Molecular Weight129.223
Monoisotopic Molecular Weight129.061220047
IUPAC Name1-isothiocyanatopentane
Traditional Name1-isothiocyanatopentane
CAS Registry Number629-12-9
SMILES
CCCCCN=C=S
InChI Identifier
InChI=1S/C6H11NS/c1-2-3-4-5-7-6-8/h2-5H2,1H3
InChI KeySGHJUJBYMSVAJY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isothiocyanates. These are organic compounds containing the isothiocyanate group, an isocyanate analogue with the general formula RN=C=S.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassIsothiocyanates
Sub ClassNot Available
Direct ParentIsothiocyanates
Alternative Parents
Substituents
  • Isothiocyanate
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point117.00 to 119.00 °C. @ 70.00 mm HgThe Good Scents Company Information System
Water Solubility0 slightlyThe Good Scents Company Information System
LogP3.172 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.12 g/LALOGPS
logP3.43ALOGPS
logP2.84ChemAxon
logS-3ALOGPS
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.36 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity39.8 m³·mol⁻¹ChemAxon
Polarizability15.45 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]+127.25631661259
DarkChem[M-H]-124.65731661259
DeepCCS[M+H]+133.85730932474
DeepCCS[M-H]-131.91130932474
DeepCCS[M-2H]-167.37230932474
DeepCCS[M+Na]+141.66230932474
AllCCS[M+H]+129.732859911
AllCCS[M+H-H2O]+125.632859911
AllCCS[M+NH4]+133.632859911
AllCCS[M+Na]+134.732859911
AllCCS[M-H]-134.932859911
AllCCS[M+Na-2H]-138.232859911
AllCCS[M+HCOO]-141.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-IsothiocyanatopentaneCCCCCN=C=S1410.5Standard polar33892256
1-IsothiocyanatopentaneCCCCCN=C=S1060.2Standard non polar33892256
1-IsothiocyanatopentaneCCCCCN=C=S1074.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1-Isothiocyanatopentane GC-MS (Non-derivatized) - 70eV, Positivesplash10-05dl-9000000000-07840e04a41d7408fe382017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Isothiocyanatopentane GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 10V, Positive-QTOFsplash10-001i-4900000000-0496303187ea50f757ba2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 20V, Positive-QTOFsplash10-00di-9200000000-5ff12e1f8832b5d54dbc2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 40V, Positive-QTOFsplash10-0596-9000000000-6d500f1c77b29fa57acb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 10V, Negative-QTOFsplash10-004i-3900000000-994f3a5d593db03c5ef42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 20V, Negative-QTOFsplash10-056r-9500000000-8e708bf67741caac86232016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 40V, Negative-QTOFsplash10-0a4i-9000000000-1aaeefea27908b1c8c7f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 10V, Positive-QTOFsplash10-001i-8900000000-5ee9462438648271fe442021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 20V, Positive-QTOFsplash10-0596-9000000000-0f4df5a78ad3aa8c5c402021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 40V, Positive-QTOFsplash10-0ab9-9000000000-e0b396463728cd79083e2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 10V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 20V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Isothiocyanatopentane 40V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-23Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
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 IDFDB017791
KNApSAcK IDC00054404
Chemspider ID62623
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound69415
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1586811
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.. .