NP-MRD: Showing NP-Card for 3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole (NP0272087)

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Record Information

Version

2.0

Created at

2022-09-08 18:35:27 UTC

Updated at

2022-09-08 18:35:27 UTC

NP-MRD ID

NP0272087

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole

Description

SCHEMBL3400592 belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole. 3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole is found in Lissoclinum fragile. SCHEMBL3400592 is a strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 39  0  0  0  0  0  0  0  0999 V2000
    5.4234   -0.2637   -0.0531 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7146    0.4949    0.8393 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3606    0.7846    0.6958 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6831    0.2821   -0.4078 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3739    0.3900   -0.8290 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2642    1.1015   -0.2175 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4193    2.4037    0.0965 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5783    3.1228    0.6450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7653    2.4711    0.8722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9654    1.1450    0.5676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9138    0.4253    0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3511   -0.8353   -0.2025 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6331   -0.9815    0.1991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5162   -2.0592    0.1964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8128   -1.9125    0.6817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1826   -0.6750    1.1571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3122    0.3934    1.1610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0122    0.2557    0.6782 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3315   -0.3434   -2.0184 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5400   -0.8595   -2.2965 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3795   -0.4879   -1.3228 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7176   -0.7564   -1.1532 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4833   -0.4714    0.0872 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2329    0.8898    1.7042 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8045    1.3837    1.4018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4185    4.1851    0.8890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5799    3.0148    1.3087 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7793   -1.6044   -0.6173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1762   -2.9944   -0.1838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5144   -2.7352    0.6911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1921   -0.4936    1.5495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5799    1.3695    1.5276 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4703   -0.4977   -2.6534 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7753   -1.4574   -3.1452 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3093   -1.3595   -1.8496 H   0  0  0  0  0  0  0  0  0  0  0  0
 20 19  1  0
 19  5  2  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  1 22  1  0
 22 21  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 18  2  0
 18 17  1  0
 17 16  2  0
 16 15  1  0
 15 14  2  0
 21 20  1  0
 11  6  1  0
 14 13  1  0
 21  4  1  0
 18 10  1  0
 20 34  1  0
 19 33  1  0
  3 25  1  0
  2 24  1  0
  1 23  1  0
 22 35  1  0
  8 26  1  0
  9 27  1  0
 12 28  1  0
 17 32  1  0
 16 31  1  0
 15 30  1  0
 14 29  1  0
M  END


  Mrv1533004231523572D          

 22 26  0  0  0  0            999 V2000
   -1.5019   -4.6223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5019   -3.7973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7874   -3.3848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0729   -3.7973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7117   -3.5424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1966   -4.2098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7117   -4.8773    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0729   -4.6223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7874   -5.0348    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9666   -2.7578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4146   -2.1447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6695   -1.3601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4765   -1.1885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0285   -1.8016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8535   -1.8016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4056   -1.1885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2125   -1.3601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4675   -2.1447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9154   -2.7578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1085   -2.5862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4410   -3.0712    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7736   -2.5862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 15 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 10 22  1  0  0  0  0
 14 22  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0272087

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N1C=C(C2=CC=CC=C12)C1=NC=CC2=C1NC1=C2C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C19H13N3/c1-3-7-16-13(6-1)15(11-21-16)18-19-14(9-10-20-18)12-5-2-4-8-17(12)22-19/h1-11,21-22H

> <INCHI_KEY>
OGIMCDMIYGVEHU-UHFFFAOYSA-N

> <FORMULA>
C19H13N3

> <MOLECULAR_WEIGHT>
283.334

> <EXACT_MASS>
283.110947431

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
31.410089941896807

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-{9H-pyrido[3,4-b]indol-1-yl}-1H-indole

> <ALOGPS_LOGP>
4.60

> <JCHEM_LOGP>
4.005050943

> <ALOGPS_LOGS>
-5.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.106022878218234

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.98748173262085

> <JCHEM_PKA_STRONGEST_BASIC>
4.283132556044118

> <JCHEM_POLAR_SURFACE_AREA>
44.47

> <JCHEM_REFRACTIVITY>
87.16600000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.43e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{9H-pyrido[3,4-b]indol-1-yl}-1H-indole

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  C   UNK     0      -2.804  -8.628   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.804  -7.088   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.470  -6.318   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.136  -7.088   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.328  -6.612   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.234  -7.858   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.328  -9.104   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -0.136  -8.628   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.470  -9.398   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.804  -5.148   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.774  -4.003   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       1.250  -2.539   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.756  -2.219   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.787  -3.363   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.327  -3.363   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.357  -2.219   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.863  -2.539   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.339  -4.003   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.309  -5.148   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.802  -4.828   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       4.557  -5.733   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       3.311  -4.828   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    4    9                                                  
CONECT    9    8    1                                                       
CONECT   10    5   11   22                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   10   14                                                  
MASTER        0    0    0    0    0    0    0    0   22    0   52    0
END

View in JSmol

Synonyms

Value	Source
1-(1H-indol-3-yl)-9H-Pyrido(3,4-b)indole	MeSH

Chemical Formula

C₁₉H₁₃N₃

Average Mass

283.3340 Da

Monoisotopic Mass

283.11095 Da

IUPAC Name

3-{9H-pyrido[3,4-b]indol-1-yl}-1H-indole

Traditional Name

3-{9H-pyrido[3,4-b]indol-1-yl}-1H-indole

CAS Registry Number

Not Available

SMILES

N1C=C(C2=CC=CC=C12)C1=NC=CC2=C1NC1=C2C=CC=C1

InChI Identifier

InChI=1S/C19H13N3/c1-3-7-16-13(6-1)15(11-21-16)18-19-14(9-10-20-18)12-5-2-4-8-17(12)22-19/h1-11,21-22H

InChI Key

OGIMCDMIYGVEHU-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Lissoclinum fragile	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Harmala alkaloids

Sub Class

Not Available

Direct Parent

Harmala alkaloids

Alternative Parents

Substituents

Harman
Beta-carboline
Pyridoindole
Indole
Indole or derivatives
Pyridine
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	4.6	ALOGPS
logP	4.01	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	12.99	ChemAxon
pKa (Strongest Basic)	4.28	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	44.47 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	87.17 m³·mol⁻¹	ChemAxon
Polarizability	31.41 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10334023

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole (NP0272087)

MOL for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

3D MOL for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

3D SDF for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

3D-SDF for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

PDB for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

3D PDB for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

SMILES for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

INCHI for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

Structure for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)

3D Structure for NP0272087 (3-{9h-pyrido[3,4-b]indol-1-yl}-1h-indole)