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Showing NP-Card for n-Amyl isothiocyanate (NP0084809)

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Record Information
Version2.0
Created at2022-04-29 05:27:03 UTC
Updated at2022-04-29 05:27:03 UTC
NP-MRD IDNP0084809
Secondary Accession NumbersNone
Natural Product Identification
Common Namen-Amyl isothiocyanate
Description1-Isothiocyanatopentane, also known as N-pentyl isothiocyanate, 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 an extremely weak basic (essentially neutral) compound (based on its pKa). 1-Isothiocyanatopentane is a green tasting compound. Outside of the human body, 1-Isothiocyanatopentane has been detected, but not quantified in, brassicas. n-Amyl isothiocyanate is found in Raphanus sativus var. niger . This could make 1-isothiocyanatopentane a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0084809 (n-Amyl isothiocyanate)


  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 NP0084809 (n-Amyl isothiocyanate)

     RDKit          3D

 19 18  0  0  0  0  0  0  0  0999 V2000
    2.6195    0.6959   -0.6030 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1644    0.7105   -0.1127 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8377   -0.7043    0.2589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5754   -0.8808    0.7714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5734   -0.4589   -0.2857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8979   -0.6650    0.2965 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8234    0.1969    0.1629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6572    1.5561    0.4969 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.9948    1.7272   -0.7394 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2581    0.1628    0.1245 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6609    0.2139   -1.6106 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5231    1.1487   -0.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1631    1.3895    0.7837 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0433   -1.3367   -0.6284 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5741   -1.0189    1.0283 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7443   -0.3891    1.7288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7191   -1.9775    0.9134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4018    0.6231   -0.4807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4463   -0.9933   -1.2242 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 NP0084809 (n-Amyl isothiocyanate)


  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>
NP0084809

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
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3D-SDF for NP0084809 (n-Amyl isothiocyanate)

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PDB for NP0084809 (n-Amyl isothiocyanate)
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 NP0084809 (n-Amyl isothiocyanate)
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SMILES for NP0084809 (n-Amyl isothiocyanate)
CCCCCN=C=S
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INCHI for NP0084809 (n-Amyl isothiocyanate)
InChI=1S/C6H11NS/c1-2-3-4-5-7-6-8/h2-5H2,1H3
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Synonyms
ValueSource
1-Isothiocyanato-pentaneHMDB
N-Amyl isothiocyanateHMDB
N-Pentyl isothiocyanateHMDB
Pentyl isothiocyanateHMDB
Chemical FormulaC6H11NS
Average Mass129.2230 Da
Monoisotopic Mass129.06122 Da
IUPAC Name1-isothiocyanatopentane
Traditional Name1-isothiocyanatopentane
CAS Registry NumberNot Available
SMILES
CCCCCN=C=S
InChI Identifier
InChI=1S/C6H11NS/c1-2-3-4-5-7-6-8/h2-5H2,1H3
InChI KeySGHJUJBYMSVAJY-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Raphanus sativus var. longipinnatusPlant
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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
HMDB IDHMDB0038433  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB017791  
KNApSAcK IDNot Available
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
Good Scents IDNot Available
References
General ReferencesNot Available