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Showing NP-Card for 3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol (NP0199793)

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Record Information
Version2.0
Created at2022-09-04 18:29:56 UTC
Updated at2022-09-04 18:29:56 UTC
NP-MRD IDNP0199793
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol
Description3-(Aminomethyl)-2,3-dihydro-1H-indol-5-ol belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene to form 2,3-dihydroindole. 3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol is found in Griffonia simplicifolia. 3-(Aminomethyl)-2,3-dihydro-1H-indol-5-ol is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0199793 (3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol)


  Mrv1533004161513132D          

 12 13  0  0  0  0            999 V2000
    0.0768   -2.3215    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
  3 12  1  0  0  0  0
  6 12  1  0  0  0  0
M  END
Download

3D MOL for NP0199793 (3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol)

     RDKit          3D

 24 25  0  0  0  0  0  0  0  0999 V2000
   -3.3623    0.6334   -0.0639 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9745    0.8460   -0.3771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1211    0.0996    0.6230 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3988   -1.3882    0.5941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5012   -1.8150   -0.4881 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6653   -1.0016   -0.4295 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9709   -1.1838   -0.8956 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9336   -0.2142   -0.7019 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6028    0.9483   -0.0403 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5516    1.9542    0.1752 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3083    1.1020    0.4088 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3224    0.1549    0.2327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4971    0.0886    0.8274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8736    1.5297    0.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6910    1.9015   -0.4362 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8080    0.4064   -1.3965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2924    0.5095    1.6229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4433   -1.6239    0.3845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0208   -1.8361    1.5476 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6815   -2.5683   -1.1692 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2392   -2.0938   -1.4162 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9505   -0.3296   -1.0520 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0741    1.8618    1.0551 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0467    2.0186    0.9306 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12  3  1  0
 12  6  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  3 17  1  1
  4 18  1  0
  4 19  1  0
  5 20  1  0
  7 21  1  0
  8 22  1  0
 10 23  1  0
 11 24  1  0
M  END
Download

3D SDF for NP0199793 (3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol)


  Mrv1533004161513132D          

 12 13  0  0  0  0            999 V2000
    0.0768   -2.3215    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
  3 12  1  0  0  0  0
  6 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0199793

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCC1CNC2=CC=C(O)C=C12

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O/c10-4-6-5-11-9-2-1-7(12)3-8(6)9/h1-3,6,11-12H,4-5,10H2

> <INCHI_KEY>
IODUMQSUUADSTG-UHFFFAOYSA-N

> <FORMULA>
C9H12N2O

> <MOLECULAR_WEIGHT>
164.208

> <EXACT_MASS>
164.094963014

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
17.86117929647618

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(aminomethyl)-2,3-dihydro-1H-indol-5-ol

> <ALOGPS_LOGP>
0.54

> <JCHEM_LOGP>
-0.2069291043344329

> <ALOGPS_LOGS>
-1.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.415862044335867

> <JCHEM_PKA_STRONGEST_BASIC>
9.34606788295192

> <JCHEM_POLAR_SURFACE_AREA>
58.28

> <JCHEM_REFRACTIVITY>
49.50130000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.02e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(aminomethyl)-2,3-dihydro-1H-indol-5-ol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0199793 (3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol)

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PDB for NP0199793 (3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol)
HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  N   UNK     0       0.143  -4.334   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.591  -2.843   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11    3    6                                                  
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END

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3D PDB for NP0199793 (3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol)
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SMILES for NP0199793 (3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol)
NCC1CNC2=CC=C(O)C=C12
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INCHI for NP0199793 (3-(aminomethyl)-2,3-dihydro-1h-indol-5-ol)
InChI=1S/C9H12N2O/c10-4-6-5-11-9-2-1-7(12)3-8(6)9/h1-3,6,11-12H,4-5,10H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC9H12N2O
Average Mass164.2080 Da
Monoisotopic Mass164.09496 Da
IUPAC Name3-(aminomethyl)-2,3-dihydro-1H-indol-5-ol
Traditional Name3-(aminomethyl)-2,3-dihydro-1H-indol-5-ol
CAS Registry NumberNot Available
SMILES
NCC1CNC2=CC=C(O)C=C12
InChI Identifier
InChI=1S/C9H12N2O/c10-4-6-5-11-9-2-1-7(12)3-8(6)9/h1-3,6,11-12H,4-5,10H2
InChI KeyIODUMQSUUADSTG-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Griffonia simplicifoliaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indolines. Indolines are compounds containing an indole moiety, which consists of pyrrolidine ring fused to benzene  to form 2,3-dihydroindole.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassIndoles and derivatives  
Sub ClassIndolines  
Direct ParentIndolines  
Alternative Parents
Substituents
  • Dihydroindole
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Phenol
    • 

  • Secondary aliphatic/aromatic amine
    • 

  • Aralkylamine
    • 

  • Benzenoid
    • 

  • Secondary amine
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Amine
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
logP0.54ALOGPS
logP-0.21ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)10.42ChemAxon
pKa (Strongest Basic)9.35ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area58.28 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity49.5 m³·mol⁻¹ChemAxon
Polarizability17.86 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound83815820  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]