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Showing NP-Card for Raphanusamide (NP0336711)

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Record Information
Version2.0
Created at2024-09-11 07:31:11 UTC
Updated at2024-09-11 07:31:11 UTC
NP-MRD IDNP0336711
Secondary Accession NumbersNone
Natural Product Identification
Common NameRaphanusamide
DescriptionRaphanusamide belongs to the class of organic compounds known as thiolactams. These are cyclic thioamides, obtained by replacing the oxygen atom from a lactam ring with sulfur. Raphanusamide is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Raphanusamide has been detected, but not quantified in, brassicas. This could make raphanusamide a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0336711 (Raphanusamide)


  Mrv0541 02241214532D          

  9  9  0  0  0  0            999 V2000
    1.0316   -1.5271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7843   -0.7013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0415   -0.5362    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2059    0.2066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0316    0.4540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0316    1.2790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2059    1.5271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2059    0.8665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0316    0.8665    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
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3D MOL for NP0336711 (Raphanusamide)

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3D SDF for NP0336711 (Raphanusamide)

  Mrv0541 02241214532D          

  9  9  0  0  0  0            999 V2000
    1.0316   -1.5271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7843   -0.7013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0415   -0.5362    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2059    0.2066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0316    0.4540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0316    1.2790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2059    1.5271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2059    0.8665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0316    0.8665    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0336711

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO\C=C1\CCNC1=S

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NOS/c1-8-4-5-2-3-7-6(5)9/h4H,2-3H2,1H3,(H,7,9)/b5-4-

> <INCHI_KEY>
FXKRKZYGKOWUNE-PLNGDYQASA-N

> <FORMULA>
C6H9NOS

> <MOLECULAR_WEIGHT>
143.207

> <EXACT_MASS>
143.040484605

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
14.875216386810429

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3Z)-3-(methoxymethylidene)pyrrolidine-2-thione

> <ALOGPS_LOGP>
0.18

> <JCHEM_LOGP>
0.283982853666667

> <ALOGPS_LOGS>
-1.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.695153802272129

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9305769164453026

> <JCHEM_POLAR_SURFACE_AREA>
21.259999999999998

> <JCHEM_REFRACTIVITY>
41.355599999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.70e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3Z)-3-(methoxymethylidene)pyrrolidine-2-thione

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0336711 (Raphanusamide)
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PDB for NP0336711 (Raphanusamide)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.926  -2.851   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.464  -1.309   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.077  -1.001   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.384   0.386   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.926   0.847   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.926   2.387   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.384   2.851   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.384   1.617   0.000  0.00  0.00           C+0
HETATM    9  S   UNK     0       1.926   1.617   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    4    7    9                                                  
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0336711 (Raphanusamide)
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SMILES for NP0336711 (Raphanusamide)
CO\C=C1\CCNC1=S
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INCHI for NP0336711 (Raphanusamide)
InChI=1S/C6H9NOS/c1-8-4-5-2-3-7-6(5)9/h4H,2-3H2,1H3,(H,7,9)/b5-4-
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H9NOS
Average Mass143.2070 Da
Monoisotopic Mass143.04048 Da
IUPAC Name(3Z)-3-(methoxymethylidene)pyrrolidine-2-thione
Traditional Name(3Z)-3-(methoxymethylidene)pyrrolidine-2-thione
CAS Registry NumberNot Available
SMILES
CO\C=C1\CCNC1=S
InChI Identifier
InChI=1S/C6H9NOS/c1-8-4-5-2-3-7-6(5)9/h4H,2-3H2,1H3,(H,7,9)/b5-4-
InChI KeyFXKRKZYGKOWUNE-PLNGDYQASA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiolactams. These are cyclic thioamides, obtained by replacing the oxygen atom from a lactam ring with sulfur.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassThiolactams  
Sub ClassNot Available
Direct ParentThiolactams  
Alternative Parents
Substituents
  • Thiolactam
    • 

  • Pyrrolidine
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Thiocarbonyl group
    • 

  • Organosulfur compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP0.18ALOGPS
logP0.28ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)11.7ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area21.26 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity41.36 m³·mol⁻¹ChemAxon
Polarizability14.88 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0041084  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB020962  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131753019  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available