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Showing metabocard for 3-Methylsulfinylpropyl isothiocyanate (HMDB0006095)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2007-04-12 22:45:27 UTC
Update Date2023-02-21 17:17:14 UTC
HMDB IDHMDB0006095
Secondary Accession Numbers
  • HMDB06095
Metabolite Identification
Common Name3-Methylsulfinylpropyl isothiocyanate
DescriptionConsumption of broccoli sprouts has shown to be effective at inhibiting Helicobacter pylori growth with sulforaphane being at least one of the active agents. Sulforaphane is an anticancer and antimicrobial compound which can be obtained by eating cruciferous vegetables such as brussel sprouts, broccoli, cauliflower, bok choy, kale, collards, arugula, broccoli sprouts, chinese broccoli, broccoli raab, kohlrabi, mustard, turnip, radish, watercress and cabbage. The enzyme myrosinase transforms glucoraphanin (a glucosinolate) into sulforaphane upon damage to the plant (such as from chewing). The young sprouts of broccoli and cauliflower are particularly rich in glucoraphanin.
Structure
Data?1676999834
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0006095 (3-Methylsulfinylpropyl isothiocyanate)

  Mrv1652302172014212D          

  9  8  0  0  0  0            999 V2000
   -3.5491    0.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8346    1.2160    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8346    2.0410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1201    0.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4056    1.2160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6912    0.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0232    1.2160    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0232    2.0410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7377    2.4535    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  2  0  0  0  0
M  END
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3D MOL for HMDB0006095 (3-Methylsulfinylpropyl isothiocyanate)

HMDB0006095
     RDKit          3D
3-Methylsulfinylpropyl isothiocyanate
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.7260    1.5244   -0.3739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0462   -0.1405   -0.4817 S   0  0  0  0  0  4  0  0  0  0  0  0
   -2.7167   -1.0834    0.5028 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2872   -0.0196   -0.2263 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4073   -1.3539   -0.2922 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8943   -1.0897   -0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1128   -0.4762    1.2416 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8675    0.5251    1.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8835    1.7834    1.3431 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4124    1.6411    0.4880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9386    2.2958   -0.2564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2714    1.7544   -1.3168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0418    0.4178    0.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1284    0.6399   -0.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3051   -1.8675   -1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0678   -2.0378    0.5019 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3249   -0.4443   -0.8469 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4488   -2.0691   -0.0275 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
M  END
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3D SDF for HMDB0006095 (3-Methylsulfinylpropyl isothiocyanate)

  Mrv1652302172014212D          

  9  8  0  0  0  0            999 V2000
   -3.5491    0.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8346    1.2160    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8346    2.0410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1201    0.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4056    1.2160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6912    0.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0232    1.2160    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0232    2.0410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7377    2.4535    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006095

> <DATABASE_NAME>
hmdb

> <SMILES>
CS(=O)CCCN=C=S

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NOS2/c1-9(7)4-2-3-6-5-8/h2-4H2,1H3

> <INCHI_KEY>
LELAOEBVZLPXAZ-UHFFFAOYSA-N

> <FORMULA>
C5H9NOS2

> <MOLECULAR_WEIGHT>
163.261

> <EXACT_MASS>
163.012555295

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
17.157465222938743

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-isothiocyanato-3-methanesulfinylpropane

> <ALOGPS_LOGP>
0.69

> <JCHEM_LOGP>
-0.29759157999999974

> <ALOGPS_LOGS>
-1.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8002741298566343

> <JCHEM_POLAR_SURFACE_AREA>
29.43

> <JCHEM_REFRACTIVITY>
44.923100000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.87e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
iberin

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0006095 (3-Methylsulfinylpropyl isothiocyanate)

HMDB0006095
     RDKit          3D
3-Methylsulfinylpropyl isothiocyanate
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.7260    1.5244   -0.3739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0462   -0.1405   -0.4817 S   0  0  0  0  0  4  0  0  0  0  0  0
   -2.7167   -1.0834    0.5028 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2872   -0.0196   -0.2263 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4073   -1.3539   -0.2922 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8943   -1.0897   -0.0569 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1128   -0.4762    1.2416 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8675    0.5251    1.3986 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8835    1.7834    1.3431 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4124    1.6411    0.4880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9386    2.2958   -0.2564 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2714    1.7544   -1.3168 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0418    0.4178    0.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1284    0.6399   -0.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3051   -1.8675   -1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0678   -2.0378    0.5019 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3249   -0.4443   -0.8469 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4488   -2.0691   -0.0275 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
M  END
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PDB for HMDB0006095 (3-Methylsulfinylpropyl isothiocyanate)

HEADER    PROTEIN                                 17-FEB-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-FEB-20         0                                  
HETATM    1  C   UNK     0      -6.625   1.500   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0      -5.291   2.270   0.000  0.00  0.00           S+0
HETATM    3  O   UNK     0      -5.291   3.810   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -3.958   1.500   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.624   2.270   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.290   1.500   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.043   2.270   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.043   3.810   0.000  0.00  0.00           C+0
HETATM    9  S   UNK     0       1.377   4.580   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0006095 (3-Methylsulfinylpropyl isothiocyanate)

COMPND    HMDB0006095
HETATM    1  C1  UNL     1      -2.726   1.524  -0.374  1.00  0.00           C  
HETATM    2  S1  UNL     1      -2.046  -0.140  -0.482  1.00  0.00           S  
HETATM    3  O1  UNL     1      -2.717  -1.083   0.503  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.287  -0.020  -0.226  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.407  -1.354  -0.292  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.894  -1.090  -0.057  1.00  0.00           C  
HETATM    7  N1  UNL     1       2.113  -0.476   1.242  1.00  0.00           N  
HETATM    8  C5  UNL     1       2.868   0.525   1.399  1.00  0.00           C  
HETATM    9  S2  UNL     1       3.883   1.783   1.343  1.00  0.00           S  
HETATM   10  H1  UNL     1      -3.412   1.641   0.488  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.939   2.296  -0.256  1.00  0.00           H  
HETATM   12  H3  UNL     1      -3.271   1.754  -1.317  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.042   0.418   0.780  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.128   0.640  -1.000  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.305  -1.868  -1.249  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.068  -2.038   0.502  1.00  0.00           H  
HETATM   17  H8  UNL     1       2.325  -0.444  -0.847  1.00  0.00           H  
HETATM   18  H9  UNL     1       2.449  -2.069  -0.027  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    3    4
CONECT    4    5   13   14
CONECT    5    6   15   16
CONECT    6    7   17   18
CONECT    7    8    8
CONECT    8    9    9
END
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SMILES for HMDB0006095 (3-Methylsulfinylpropyl isothiocyanate)

CS(=O)CCCN=C=S
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INCHI for HMDB0006095 (3-Methylsulfinylpropyl isothiocyanate)

InChI=1S/C5H9NOS2/c1-9(7)4-2-3-6-5-8/h2-4H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Isothiocyanatopropyl methyl sulfoxideChEBI
IMSPChEBI
MethylsulfinylpropylisothiocyanateChEBI
3-Isothiocyanatopropyl methyl sulphoxideGenerator
Methylsulfinylpropylisothiocyanic acidGenerator
MethylsulphinylpropylisothiocyanateGenerator
Methylsulphinylpropylisothiocyanic acidGenerator
3-Methylsulfinylpropyl isothiocyanic acidGenerator
3-Methylsulphinylpropyl isothiocyanateGenerator
3-Methylsulphinylpropyl isothiocyanic acidGenerator
1-Isothiocyanato-3-(methylsulphinyl)propaneMeSH
1-Isothiocyanato-3-(methylsulfinyl)propaneMeSH
(R)-1-Isothiocyanato-3-(methylsulphinyl)propaneGenerator
Chemical FormulaC5H9NOS2
Average Molecular Weight163.261
Monoisotopic Molecular Weight163.012555295
IUPAC Name1-isothiocyanato-3-methanesulfinylpropane
Traditional Nameiberin
CAS Registry Number505-44-2
SMILES
CS(=O)CCCN=C=S
InChI Identifier
InChI=1S/C5H9NOS2/c1-9(7)4-2-3-6-5-8/h2-4H2,1H3
InChI KeyLELAOEBVZLPXAZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sulfoxides. Sulfoxides are compounds containing a sulfoxide functional group, with the structure RS(=O)R' (R,R' not H).
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassSulfoxides
Sub ClassNot Available
Direct ParentSulfoxides
Alternative Parents
Substituents
  • Sulfoxide
  • Isothiocyanate
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Sulfinyl compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.09 +/- 0.08 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008196
KNApSAcK IDC00047246
Chemspider ID10023
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10455
PDB IDNot Available
ChEBI ID89494
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