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Showing NP-Card for Lepidine B (NP0047441)

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Record Information
Version2.0
Created at2022-03-17 20:40:15 UTC
Updated at2022-03-17 20:40:16 UTC
NP-MRD IDNP0047441
Secondary Accession NumbersNone
Natural Product Identification
Common NameLepidine B
DescriptionLepidine B belongs to the class of organic compounds known as diphenylethers. These are aromatic compounds containing two benzene rings linked to each other through an ether group. Lepidine B is a very strong basic compound (based on its pKa). Outside of the human body, Lepidine B has been detected, but not quantified in, brassicas and garden cress. Lepidine B is found in Lepidium satisvum. This could make lepidine b a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0047441 (Lepidine B)


  Mrv0541 05061306392D          

 26 29  0  0  0  0            999 V2000
   -1.4289    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   10.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   10.8911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    8.0036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    9.6536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    4.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    4.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7346   10.2010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3221    9.4866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    8.0036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0000    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   10.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    8.4161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    9.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0000    9.6536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    5.4562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    5.4562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1826   10.8141    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5152    9.6581    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    8.4161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    9.2411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  8  7  2  0  0  0  0
 10  9  2  0  0  0  0
 14  3  1  0  0  0  0
 14 11  2  0  0  0  0
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 15  4  1  0  0  0  0
 15 13  1  0  0  0  0
 16  5  2  0  0  0  0
 16 11  1  0  0  0  0
 17  6  2  0  0  0  0
 18 12  1  0  0  0  0
 19 13  1  0  0  0  0
 20 15  2  0  0  0  0
 20 17  1  0  0  0  0
 21  7  1  0  0  0  0
 21 18  2  0  0  0  0
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 22 18  1  0  0  0  0
 23  9  1  0  0  0  0
 23 19  2  0  0  0  0
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 25 17  1  0  0  0  0
 26 16  1  0  0  0  0
 26 20  1  0  0  0  0
M  END
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3D MOL for NP0047441 (Lepidine B)

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3D SDF for NP0047441 (Lepidine B)

  Mrv0541 05061306392D          

 26 29  0  0  0  0            999 V2000
   -1.4289    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   10.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    6.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   10.8911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    8.0036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    9.6536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    4.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    4.6715    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7346   10.2010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3221    9.4866    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    8.0036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.7661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   10.8911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    7.1786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   10.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    8.4161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    9.2411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   10.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    9.6536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    5.4562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    5.4562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1826   10.8141    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5152    9.6581    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    8.4161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    9.2411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  8  7  2  0  0  0  0
 10  9  2  0  0  0  0
 14  3  1  0  0  0  0
 14 11  2  0  0  0  0
 14 12  1  0  0  0  0
 15  4  1  0  0  0  0
 15 13  1  0  0  0  0
 16  5  2  0  0  0  0
 16 11  1  0  0  0  0
 17  6  2  0  0  0  0
 18 12  1  0  0  0  0
 19 13  1  0  0  0  0
 20 15  2  0  0  0  0
 20 17  1  0  0  0  0
 21  7  1  0  0  0  0
 21 18  2  0  0  0  0
 22  8  1  0  0  0  0
 22 18  1  0  0  0  0
 23  9  1  0  0  0  0
 23 19  2  0  0  0  0
 24 10  1  0  0  0  0
 24 19  1  0  0  0  0
 25 17  1  0  0  0  0
 26 16  1  0  0  0  0
 26 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0047441

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC=CC(CC2=NC=CN2)=C1OC1=CC=CC(CC2=NC=CN2)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H18N4O2/c25-17-6-2-4-15(13-19-23-9-10-24-19)20(17)26-16-5-1-3-14(11-16)12-18-21-7-8-22-18/h1-11,25H,12-13H2,(H,21,22)(H,23,24)

> <INCHI_KEY>
RQNSAUQJLRAUMV-UHFFFAOYSA-N

> <FORMULA>
C20H18N4O2

> <MOLECULAR_WEIGHT>
346.3825

> <EXACT_MASS>
346.14297584

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
36.280465907600586

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(1H-imidazol-2-ylmethyl)-2-[3-(1H-imidazol-2-ylmethyl)phenoxy]phenol

> <ALOGPS_LOGP>
3.53

> <JCHEM_LOGP>
2.6347213200330537

> <ALOGPS_LOGS>
-3.92

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
13.092058430083739

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.48377347464278

> <JCHEM_PKA_STRONGEST_BASIC>
7.304905007993754

> <JCHEM_POLAR_SURFACE_AREA>
86.82000000000001

> <JCHEM_REFRACTIVITY>
98.5145

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.19e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(1H-imidazol-2-ylmethyl)-2-[3-(1H-imidazol-2-ylmethyl)phenoxy]phenol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0047441 (Lepidine B)
Download
PDB for NP0047441 (Lepidine B)
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      -2.667  13.400   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  19.560   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  12.630   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  20.330   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  14.940   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  18.020   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.564   8.720   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.104   8.720   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.105  19.042   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.335  17.708   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000  14.940   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  12.630   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334  20.330   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000  13.400   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000  19.560   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.334  15.710   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  17.250   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334  11.090   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.667  19.560   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000  18.020   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       0.088  10.185   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       2.580  10.185   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0      -4.074  20.186   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0      -2.828  18.028   0.000  0.00  0.00           N+0
HETATM   25  O   UNK     0       1.334  15.710   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -1.334  17.250   0.000  0.00  0.00           O+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1   14                                                       
CONECT    4    2   15                                                       
CONECT    5    1   16                                                       
CONECT    6    2   17                                                       
CONECT    7    8   21                                                       
CONECT    8    7   22                                                       
CONECT    9   10   23                                                       
CONECT   10    9   24                                                       
CONECT   11   14   16                                                       
CONECT   12   14   18                                                       
CONECT   13   15   19                                                       
CONECT   14    3   11   12                                                  
CONECT   15    4   13   20                                                  
CONECT   16    5   11   26                                                  
CONECT   17    6   20   25                                                  
CONECT   18   12   21   22                                                  
CONECT   19   13   23   24                                                  
CONECT   20   15   17   26                                                  
CONECT   21    7   18                                                       
CONECT   22    8   18                                                       
CONECT   23    9   19                                                       
CONECT   24   10   19                                                       
CONECT   25   17                                                            
CONECT   26   16   20                                                       
MASTER        0    0    0    0    0    0    0    0   26    0   58    0
END

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3D PDB for NP0047441 (Lepidine B)
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SMILES for NP0047441 (Lepidine B)
OC1=CC=CC(CC2=NC=CN2)=C1OC1=CC=CC(CC2=NC=CN2)=C1
Download
INCHI for NP0047441 (Lepidine B)
InChI=1S/C20H18N4O2/c25-17-6-2-4-15(13-19-23-9-10-24-19)20(17)26-16-5-1-3-14(11-16)12-18-21-7-8-22-18/h1-11,25H,12-13H2,(H,21,22)(H,23,24)
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SynonymsNot Available
Chemical FormulaC20H18N4O2
Average Mass346.3825 Da
Monoisotopic Mass346.14298 Da
IUPAC Name3-(1H-imidazol-2-ylmethyl)-2-[3-(1H-imidazol-2-ylmethyl)phenoxy]phenol
Traditional Name3-(1H-imidazol-2-ylmethyl)-2-[3-(1H-imidazol-2-ylmethyl)phenoxy]phenol
CAS Registry NumberNot Available
SMILES
OC1=CC=CC(CC2=NC=CN2)=C1OC1=CC=CC(CC2=NC=CN2)=C1
InChI Identifier
InChI=1S/C20H18N4O2/c25-17-6-2-4-15(13-19-23-9-10-24-19)20(17)26-16-5-1-3-14(11-16)12-18-21-7-8-22-18/h1-11,25H,12-13H2,(H,21,22)(H,23,24)
InChI KeyRQNSAUQJLRAUMV-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Lepidium satisvumPlant
Lepidium sativumFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diphenylethers. These are aromatic compounds containing two benzene rings linked to each other through an ether group.
KingdomOrganic compounds  
Super ClassBenzenoids  
ClassBenzene and substituted derivatives  
Sub ClassDiphenylethers  
Direct ParentDiphenylethers  
Alternative Parents
Substituents
  • Diphenylether
    • 

  • Diaryl ether
    • 

  • Phenoxy compound
    • 

  • Phenol ether
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Phenol
    • 

  • Azole
    • 

  • Imidazole
    • 

  • Heteroaromatic compound
    • 

  • Ether
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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
logP3.53ALOGPS
logP2.63ChemAxon
logS-3.9ALOGPS
pKa (Strongest Acidic)8.48ChemAxon
pKa (Strongest Basic)7.3ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.82 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity98.51 m³·mol⁻¹ChemAxon
Polarizability36.28 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDHMDB0032715  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB010676  
KNApSAcK IDC00028459  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound100927764  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available