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Showing NP-Card for 3-Methylene-indolenine (NP0091540)

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Record Information
Version2.0
Created at2022-05-11 18:40:48 UTC
Updated at2022-05-11 18:40:48 UTC
NP-MRD IDNP0091540
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Methylene-indolenine
Description3-Methylene-indolenine belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. An indole that consists of 3H-indole bearing a methylene substituent at position 3. 3-Methylene-indolenine was first documented in 1999 (PMID: 10383923). 3-Methylene-indolenine is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0091540 (3-Methylene-indolenine)


  Mrv0541 02241201492D          

 10 11  0  0  0  0            999 V2000
    9.3522   -6.0185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3522   -6.8435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6376   -5.6060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6376   -7.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9232   -6.0185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9232   -6.8435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1367   -5.7637    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.6215   -6.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1366   -7.0985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3914   -7.8832    0.0000 C   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  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  1  1  0  0  0  0
  2  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  8  1  0  0  0  0
  9  2  1  0  0  0  0
 10  9  2  0  0  0  0
M  END
Download

3D MOL for NP0091540 (3-Methylene-indolenine)

     RDKit          3D

 17 18  0  0  0  0  0  0  0  0999 V2000
    2.5311   -0.9590    0.1307 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6479    0.0184    0.1528 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8798    1.4440    0.3244 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7382    2.0096    0.2796 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3259    1.1158    0.0878 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7135    1.2368   -0.0265 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5202    0.1332   -0.2167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9820   -1.1327   -0.3010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6230   -1.2493   -0.1888 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2096   -0.1521    0.0031 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1985   -1.9629   -0.0057 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5809   -0.6828    0.2560 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8548    1.9341    0.4654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1380    2.2350    0.0399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5952    0.2249   -0.3055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6074   -2.0078   -0.4505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1355   -2.2053   -0.2450 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
 10  5  1  0
  1 11  1  0
  1 12  1  0
  3 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
Download

3D SDF for NP0091540 (3-Methylene-indolenine)


  Mrv0541 02241201492D          

 10 11  0  0  0  0            999 V2000
    9.3522   -6.0185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3522   -6.8435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6376   -5.6060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6376   -7.2560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9232   -6.0185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9232   -6.8435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1367   -5.7637    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.6215   -6.4311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1366   -7.0985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3914   -7.8832    0.0000 C   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  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  1  1  0  0  0  0
  2  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  8  1  0  0  0  0
  9  2  1  0  0  0  0
 10  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0091540

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C=C1C=NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C9H7N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6H,1H2

> <INCHI_KEY>
BCNUXXXHEIUHJB-UHFFFAOYSA-N

> <FORMULA>
C9H7N

> <MOLECULAR_WEIGHT>
129.1586

> <EXACT_MASS>
129.057849229

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
14.083628644599568

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylidene-3H-indole

> <ALOGPS_LOGP>
2.40

> <JCHEM_LOGP>
2.2309315876666664

> <ALOGPS_LOGS>
-2.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.306820778042735

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
43.505700000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.36e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methyleneindolenine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0091540 (3-Methylene-indolenine)

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PDB for NP0091540 (3-Methylene-indolenine)
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      17.457 -11.235   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.457 -12.775   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.124 -10.465   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.124 -13.545   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.790 -11.235   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.790 -12.775   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      18.922 -10.759   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      19.827 -12.005   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.922 -13.251   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.397 -14.715   0.000  0.00  0.00           C+0
CONECT    1    3    7    2                                                  
CONECT    2    4    1    9                                                  
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5                                                       
CONECT    7    1    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    2   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END

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3D PDB for NP0091540 (3-Methylene-indolenine)
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SMILES for NP0091540 (3-Methylene-indolenine)
C=C1C=NC2=CC=CC=C12
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INCHI for NP0091540 (3-Methylene-indolenine)
InChI=1S/C9H7N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6H,1H2
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View in JSmol
Synonyms
ValueSource
3-Methylene-3H-indoleHMDB
3-MethyleneindolenineHMDB
3-Methyleneindolenine, conjugate acidHMDB
3-Methylene-indolenineMeSH
Chemical FormulaC9H7N
Average Mass129.1586 Da
Monoisotopic Mass129.05785 Da
IUPAC Name3-methylidene-3H-indole
Traditional Name3-methyleneindolenine
CAS Registry NumberNot Available
SMILES
C=C1C=NC2=CC=CC=C12
InChI Identifier
InChI=1S/C9H7N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6H,1H2
InChI KeyBCNUXXXHEIUHJB-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassIndoles and derivatives  
Sub ClassNot Available
Direct ParentIndoles and derivatives  
Alternative Parents
Substituents
  • Indole or derivatives
    • 

  • Benzenoid
    • 

  • Azacycle
    • 

  • Organic 1,3-dipolar compound
    • 

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

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organonitrogen compound
    • 

  • Imine
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
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
logP2.4ALOGPS
logP2.23ChemAxon
logS-2.7ALOGPS
pKa (Strongest Basic)5.31ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.36 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity43.51 m³·mol⁻¹ChemAxon
Polarizability14.08 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0011664  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028355  
KNApSAcK IDNot Available
Chemspider ID148991  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound170404  
PDB IDNot Available
ChEBI ID63905  
Good Scents IDNot Available
References
General References
  1. Lanza DL, Code E, Crespi CL, Gonzalez FJ, Yost GS: Specific dehydrogenation of 3-methylindole and epoxidation of naphthalene by recombinant human CYP2F1 expressed in lymphoblastoid cells. Drug Metab Dispos. 1999 Jul;27(7):798-803. [PubMed:10383923  ]