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Showing NP-Card for Ibervirin (NP0047950)

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Record Information
Version2.0
Created at2022-03-17 20:48:35 UTC
Updated at2022-03-17 20:48:36 UTC
NP-MRD IDNP0047950
Secondary Accession NumbersNone
Natural Product Identification
Common NameIbervirin
DescriptionIbervirin, also known as fema 3312, 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. Ibervirin is an extremely weak basic (essentially neutral) compound (based on its pKa). Ibervirin is an earthy, horseradish, and sulfurous tasting compound. Outside of the human body, Ibervirin is found, on average, in the highest concentration within kohlrabis. Ibervirin has also been detected, but not quantified in, several different foods, such as cabbages, root vegetables, horseradish, cauliflowers, and brassicas. This could make ibervirin a potential biomarker for the consumption of these foods. Ibervirin is found in Brassica oleracea. Found in hydrolysates of crucifer seedsand is also found in cabbage, cauliflower, kohlrabi, horse radish (Armoracia lapathifolia), Japanese horseradish (Wasabi japonica) and radish (Rapharius sativus).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0047950 (Ibervirin)


  Mrv1652302262014522D          

  8  7  0  0  0  0            999 V2000
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2374    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
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    1.5395    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  6  3  1  0  0  0  0
  8  1  1  0  0  0  0
  8  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  5  2  0  0  0  0
M  END
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3D MOL for NP0047950 (Ibervirin)

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3D SDF for NP0047950 (Ibervirin)

  Mrv1652302262014522D          

  8  7  0  0  0  0            999 V2000
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2374    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
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    1.5395    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  6  3  1  0  0  0  0
  8  1  1  0  0  0  0
  8  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  5  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0047950

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CSCCCN=C=S

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NS2/c1-8-4-2-3-6-5-7/h2-4H2,1H3

> <INCHI_KEY>
LDKSCZJUIURGMW-UHFFFAOYSA-N

> <FORMULA>
C5H9NS2

> <MOLECULAR_WEIGHT>
147.262

> <EXACT_MASS>
147.017640673

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
16.52417550465011

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-isothiocyanato-3-(methylsulfanyl)propane

> <ALOGPS_LOGP>
2.52

> <JCHEM_LOGP>
2.0778863870000004

> <ALOGPS_LOGS>
-2.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-3.013889208168397

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
43.166399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.70e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-isothiocyanato-3-(methylsulfanyl)propane

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0047950 (Ibervirin)
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PDB for NP0047950 (Ibervirin)
HEADER    PROTEIN                                 26-FEB-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-FEB-20         0                                  
HETATM    1  C   UNK     0       6.311   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.976   2.104   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      -1.691   2.104   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -0.357   1.334   0.000  0.00  0.00           N+0
HETATM    7  S   UNK     0      -3.025   2.874   0.000  0.00  0.00           S+0
HETATM    8  S   UNK     0       4.977   1.334   0.000  0.00  0.00           S+0
CONECT    1    8                                                            
CONECT    2    3    4                                                       
CONECT    3    2    6                                                       
CONECT    4    2    8                                                       
CONECT    5    6    7                                                       
CONECT    6    3    5                                                       
CONECT    7    5                                                            
CONECT    8    1    4                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0047950 (Ibervirin)
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SMILES for NP0047950 (Ibervirin)
CSCCCN=C=S
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INCHI for NP0047950 (Ibervirin)
InChI=1S/C5H9NS2/c1-8-4-2-3-6-5-7/h2-4H2,1H3
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Synonyms
ValueSource
1-Isothiocyanato-3-(methylsulfanyl)propaneHMDB
1-Isothiocyanato-3-(methylthio)-propaneHMDB
3-(Methylthio)propyl isothiocyanateHMDB
3-Methylmercaptopropyl isothiocyanateHMDB
3-MethylthiopropylHMDB
3-Methylthiopropyl isothiocyanateHMDB
FEMA 3312HMDB
Isothiocyanic acid, 3-(methylthio)propyl esterHMDB
1-Isothiocyanato-3-(methylsulphanyl)propaneGenerator
IberverinMeSH
Chemical FormulaC5H9NS2
Average Mass147.2620 Da
Monoisotopic Mass147.01764 Da
IUPAC Name1-isothiocyanato-3-(methylsulfanyl)propane
Traditional Name1-isothiocyanato-3-(methylsulfanyl)propane
CAS Registry Number505-79-3
SMILES
CSCCCN=C=S
InChI Identifier
InChI=1S/C5H9NS2/c1-8-4-2-3-6-5-7/h2-4H2,1H3
InChI KeyLDKSCZJUIURGMW-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Armoracia rusticanaFooDB
Brassica oleraceaLOTUS Database
Brassica oleracea var. botrytisFooDB
    • L. Valettea X. Fernandez, S. Poulain, A.-M. Loiseau, L. Lizzani-Cuvelier, R. Levieil, L. Restier....
Brassica oleracea var. capitataFooDB
Brassica oleracea var. gongylodesFooDB
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
    • 

  • Dialkylthioether
    • 

  • Organic 1,3-dipolar compound
    • 

  • Propargyl-type 1,3-dipolar organic compound
    • 

  • Sulfenyl compound
    • 

  • Thioether
    • 

  • 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
logP2.52ALOGPS
logP2.08ChemAxon
logS-2.9ALOGPS
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.36 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity43.17 m³·mol⁻¹ChemAxon
Polarizability16.52 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0034370  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012744  
KNApSAcK IDNot Available
Chemspider ID56142  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound62351  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available