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Showing metabocard for 5-Isothiocyanato-1-pentene (HMDB0034300)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 19:06:23 UTC
Update Date2023-02-21 17:24:09 UTC
HMDB IDHMDB0034300
Secondary Accession Numbers
  • HMDB34300
Metabolite Identification
Common Name5-Isothiocyanato-1-pentene
Description5-Isothiocyanato-1-pentene 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. 5-Isothiocyanato-1-pentene is a horseradish and mustard tasting compound. 5-Isothiocyanato-1-pentene has been detected, but not quantified in, several different foods, such as white cabbages (Brassica oleracea L. var. capitata L. f. alba DC.), horseradishes (Armoracia rusticana), rocket salad (ssp.), wasabis (Wasabia japonica), and brassicas. This could make 5-isothiocyanato-1-pentene a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 5-Isothiocyanato-1-pentene.
Structure
Data?1677000249
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034300 (5-Isothiocyanato-1-pentene)


  Mrv1652310191722222D          

  8  7  0  0  0  0            999 V2000
    6.6515    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9370    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  2  0  0  0  0
  2  5  1  0  0  0  0
  2  8  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
Download

3D MOL for HMDB0034300 (5-Isothiocyanato-1-pentene)

HMDB0034300
     RDKit          3D
5-Isothiocyanato-1-pentene
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.8397    1.1061    0.1249 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0877    0.1770    0.6788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9544   -0.4016   -0.0624 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3717   -0.1877    0.6308 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4557   -0.8200   -0.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7644   -0.6748    0.3525 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6643    0.0474   -0.1636 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4427    1.4554   -0.3807 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6868    1.5707    0.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6285    1.4500   -0.8797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3257   -0.1409    1.6774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0873   -1.5189   -0.1572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8500   -0.0275   -1.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4024   -0.6464    1.6254 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6143    0.8934    0.6977 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4818   -0.3697   -1.2380 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2628   -1.9126   -0.3760 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
  2 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
M  END
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3D SDF for HMDB0034300 (5-Isothiocyanato-1-pentene)


  Mrv1652310191722222D          

  8  7  0  0  0  0            999 V2000
    6.6515    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9370    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  2  0  0  0  0
  2  5  1  0  0  0  0
  2  8  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034300

> <DATABASE_NAME>
hmdb

> <SMILES>
C=CCCCN=C=S

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NS/c1-2-3-4-5-7-6-8/h2H,1,3-5H2

> <INCHI_KEY>
DBISBKDNOKIADM-UHFFFAOYSA-N

> <FORMULA>
C6H9NS

> <MOLECULAR_WEIGHT>
127.207

> <EXACT_MASS>
127.045569983

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
14.53243821304148

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-isothiocyanatopent-1-ene

> <ALOGPS_LOGP>
2.98

> <JCHEM_LOGP>
2.534129747333333

> <ALOGPS_LOGS>
-3.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.885429019093431

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
39.8478

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.70e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-pentene, 5-isothiocyanato-

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0034300 (5-Isothiocyanato-1-pentene)

HMDB0034300
     RDKit          3D
5-Isothiocyanato-1-pentene
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.8397    1.1061    0.1249 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0877    0.1770    0.6788 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9544   -0.4016   -0.0624 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3717   -0.1877    0.6308 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4557   -0.8200   -0.2162 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7644   -0.6748    0.3525 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6643    0.0474   -0.1636 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4427    1.4554   -0.3807 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6868    1.5707    0.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6285    1.4500   -0.8797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3257   -0.1409    1.6774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0873   -1.5189   -0.1572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8500   -0.0275   -1.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4024   -0.6464    1.6254 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6143    0.8934    0.6977 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4818   -0.3697   -1.2380 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2628   -1.9126   -0.3760 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
  2 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
M  END
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PDB for HMDB0034300 (5-Isothiocyanato-1-pentene)

HEADER    PROTEIN                                 19-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-OCT-17         0                                  
HETATM    1  S   UNK     0      12.416   0.770   0.000  0.00  0.00           S+0
HETATM    2  N   UNK     0       9.748  -0.770   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       7.081  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.747   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.415   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.414  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.080   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.082   0.000   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    5    8                                                       
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    2    3                                                       
CONECT    6    4    7                                                       
CONECT    7    6                                                            
CONECT    8    1    2                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0034300 (5-Isothiocyanato-1-pentene)

COMPND    HMDB0034300
HETATM    1  C1  UNL     1      -2.840   1.106   0.125  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.088   0.177   0.679  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.954  -0.402  -0.062  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.372  -0.188   0.631  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.456  -0.820  -0.216  1.00  0.00           C  
HETATM    6  N1  UNL     1       2.764  -0.675   0.352  1.00  0.00           N  
HETATM    7  C6  UNL     1       3.664   0.047  -0.164  1.00  0.00           C  
HETATM    8  S1  UNL     1       4.443   1.455  -0.381  1.00  0.00           S  
HETATM    9  H1  UNL     1      -3.687   1.571   0.617  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.629   1.450  -0.880  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.326  -0.141   1.677  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.087  -1.519  -0.157  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.850  -0.027  -1.084  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.402  -0.646   1.625  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.614   0.893   0.698  1.00  0.00           H  
HETATM   16  H8  UNL     1       1.482  -0.370  -1.238  1.00  0.00           H  
HETATM   17  H9  UNL     1       1.263  -1.913  -0.376  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6    7    7
CONECT    7    8    8
END
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SMILES for HMDB0034300 (5-Isothiocyanato-1-pentene)

C=CCCCN=C=S
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INCHI for HMDB0034300 (5-Isothiocyanato-1-pentene)

InChI=1S/C6H9NS/c1-2-3-4-5-7-6-8/h2H,1,3-5H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
4-Pentenyl isothiocyanateHMDB
5-isothiocyano-1-PenteneHMDB
Chemical FormulaC6H9NS
Average Molecular Weight127.207
Monoisotopic Molecular Weight127.045569983
IUPAC Name5-isothiocyanatopent-1-ene
Traditional Name1-pentene, 5-isothiocyanato-
CAS Registry Number18060-79-2
SMILES
C=CCCCN=C=S
InChI Identifier
InChI=1S/C6H9NS/c1-2-3-4-5-7-6-8/h2H,1,3-5H2
InChI KeyDBISBKDNOKIADM-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 Point182.00 to 183.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility0.16 mg/mL at 20 °CNot Available
LogP3.014 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.077 g/LALOGPS
logP2.98ALOGPS
logP2.53ChemAxon
logS-3.2ALOGPS
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.36 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity39.85 m³·mol⁻¹ChemAxon
Polarizability14.53 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]+127.48631661259
DarkChem[M-H]-123.98231661259
DeepCCS[M+H]+131.14230932474
DeepCCS[M-H]-129.18330932474
DeepCCS[M-2H]-164.67530932474
DeepCCS[M+Na]+138.95430932474
AllCCS[M+H]+128.932859911
AllCCS[M+H-H2O]+124.832859911
AllCCS[M+NH4]+132.932859911
AllCCS[M+Na]+134.032859911
AllCCS[M-H]-132.332859911
AllCCS[M+Na-2H]-135.632859911
AllCCS[M+HCOO]-139.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Isothiocyanato-1-penteneC=CCCCN=C=S1593.1Standard polar33892256
5-Isothiocyanato-1-penteneC=CCCCN=C=S1055.2Standard non polar33892256
5-Isothiocyanato-1-penteneC=CCCCN=C=S1069.0Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - 5-Isothiocyanato-1-pentene EI-B (Non-derivatized)splash10-0076-9100000000-b80ff5278e20ade2da972017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 5-Isothiocyanato-1-pentene EI-B (Non-derivatized)splash10-0076-9100000000-b80ff5278e20ade2da972018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Isothiocyanato-1-pentene GC-MS (Non-derivatized) - 70eV, Positivesplash10-004l-9000000000-2f496c6688974064260c2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Isothiocyanato-1-pentene 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 - 5-Isothiocyanato-1-pentene 10V, Positive-QTOFsplash10-004i-6900000000-396a21b2ef411234ccd82017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 20V, Positive-QTOFsplash10-014i-9100000000-f9063e8cfa24ee6a53eb2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 40V, Positive-QTOFsplash10-0gbc-9000000000-02ccd98ce72f4be0ccde2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 10V, Negative-QTOFsplash10-004i-3900000000-bf4da00bcf6d39df67bb2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 20V, Negative-QTOFsplash10-0a7i-9300000000-ca6cfce482de77095a832017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 40V, Negative-QTOFsplash10-0a4i-9000000000-66c809b0364da6698de02017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 10V, Positive-QTOFsplash10-056r-9400000000-9ae927459c0e6b997c5a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 20V, Positive-QTOFsplash10-00kf-9000000000-0f81f047ff86010784f72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 40V, Positive-QTOFsplash10-0avi-9000000000-7abc22059487ca72b0be2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 10V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 20V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Isothiocyanato-1-pentene 40V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart 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 IDFDB012643
KNApSAcK IDC00052675
Chemspider ID78870
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound87436
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1551741
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.. .