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Showing NP-Card for Harmalacidine (NP0138456)

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Record Information
Version1.0
Created at2022-06-29 17:30:22 UTC
Updated at2022-06-29 17:30:22 UTC
NP-MRD IDNP0138456
Secondary Accession NumbersNone
Natural Product Identification
Common NameHarmalacidine
DescriptionHarmalacidine belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety. Harmalacidine is found in Peganum harmala. Harmalacidine is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0138456 (Harmalacidine)


  Mrv1533004161507262D          

 16 18  0  0  0  0            999 V2000
   -0.6473   -3.1008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3924   -2.3162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4146   -2.1447    0.0000 C   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 N   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
    4.1704   -3.5424    0.0000 O   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
    0.9666   -2.7578    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  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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  7 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  2  0  0  0  0
  3 16  1  0  0  0  0
M  END
Download

3D MOL for NP0138456 (Harmalacidine)

     RDKit          3D

 28 30  0  0  0  0  0  0  0  0999 V2000
    4.9952    0.2102   -0.6428 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1028    0.1694    0.4296 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7287    0.0501    0.2308 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2475   -0.0290   -1.0591 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8867   -0.1484   -1.2962 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0326   -0.1856   -0.2111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3603   -0.2975   -0.1168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6847   -0.2833    1.2228 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5596   -0.1685    1.9446 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4700   -0.1100    1.0828 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8461    0.0096    1.2859 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0754   -0.3841    1.6643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3898   -0.3728    2.8810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0591   -0.4960    0.6425 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7306    0.0693   -0.6448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3912   -0.4147   -1.1586 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0252    0.1459   -0.2383 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7675   -0.6430   -1.3193 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8122    1.1394   -1.2188 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9198    0.0008   -1.8975 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4866   -0.2121   -2.2990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5246   -0.1337    2.9860 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2183    0.0712    2.2945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9729   -0.9764    0.8544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6327    1.1827   -0.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5273   -0.0591   -1.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1636    0.1921   -2.0611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4676   -1.4732   -1.4947 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  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  1  0
 10 11  2  0
  8 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 11  3  1  0
 10  6  1  0
 16  7  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  4 20  1  0
  5 21  1  0
  9 22  1  0
 11 23  1  0
 14 24  1  0
 15 25  1  0
 15 26  1  0
 16 27  1  0
 16 28  1  0
M  END
Download

3D SDF for NP0138456 (Harmalacidine)


  Mrv1533004161507262D          

 16 18  0  0  0  0            999 V2000
   -0.6473   -3.1008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3924   -2.3162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4146   -2.1447    0.0000 C   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 N   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
    4.1704   -3.5424    0.0000 O   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
    0.9666   -2.7578    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  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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  7 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  2  0  0  0  0
  3 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0138456

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C2C3=C(NC2=C1)C(=O)NCC3

> <INCHI_IDENTIFIER>
InChI=1S/C12H12N2O2/c1-16-7-2-3-8-9-4-5-13-12(15)11(9)14-10(8)6-7/h2-3,6,14H,4-5H2,1H3,(H,13,15)

> <INCHI_KEY>
MWEGNYFSTKOOSD-UHFFFAOYSA-N

> <FORMULA>
C12H12N2O2

> <MOLECULAR_WEIGHT>
216.24

> <EXACT_MASS>
216.089877634

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
22.964921989431076

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-methoxy-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-1-one

> <ALOGPS_LOGP>
1.37

> <JCHEM_LOGP>
0.9485425333333335

> <ALOGPS_LOGS>
-2.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.454076402752047

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.91075044440036

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3754787377693738

> <JCHEM_POLAR_SURFACE_AREA>
54.12

> <JCHEM_REFRACTIVITY>
60.76989999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.07e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-methoxy-2H,3H,4H,9H-pyrido[3,4-b]indol-1-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0138456 (Harmalacidine)

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PDB for NP0138456 (Harmalacidine)
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  C   UNK     0      -1.208  -5.788   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.732  -4.324   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.774  -4.003   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.250  -2.539   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.756  -2.219   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.787  -3.363   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.327  -3.363   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.357  -2.219   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.863  -2.539   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       8.339  -4.003   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       7.309  -5.148   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       7.785  -6.612   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.802  -4.828   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       4.557  -5.733   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       3.311  -4.828   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.804  -5.148   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   16                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   15                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    7   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14    6   16                                                  
CONECT   16   15    3                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   36    0
END

Download
3D PDB for NP0138456 (Harmalacidine)
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SMILES for NP0138456 (Harmalacidine)
COC1=CC=C2C3=C(NC2=C1)C(=O)NCC3
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INCHI for NP0138456 (Harmalacidine)
InChI=1S/C12H12N2O2/c1-16-7-2-3-8-9-4-5-13-12(15)11(9)14-10(8)6-7/h2-3,6,14H,4-5H2,1H3,(H,13,15)
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View in JSmol
SynonymsNot Available
Chemical FormulaC12H12N2O2
Average Mass216.2400 Da
Monoisotopic Mass216.08988 Da
IUPAC Name7-methoxy-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-1-one
Traditional Name7-methoxy-2H,3H,4H,9H-pyrido[3,4-b]indol-1-one
CAS Registry Number26579-69-1
SMILES
COC1=CC=C2C3=C(NC2=C1)C(=O)NCC3
InChI Identifier
InChI=1S/C12H12N2O2/c1-16-7-2-3-8-9-4-5-13-12(15)11(9)14-10(8)6-7/h2-3,6,14H,4-5H2,1H3,(H,13,15)
InChI KeyMWEGNYFSTKOOSD-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
Peganum harmalaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassIndoles and derivatives  
Sub ClassPyridoindoles  
Direct ParentBeta carbolines  
Alternative Parents
Substituents
  • Beta-carboline
    • 

  • Indolecarboxylic acid derivative
    • 

  • 3-alkylindole
    • 

  • Indole
    • 

  • 2-heteroaryl carboxamide
    • 

  • Anisole
    • 

  • Alkyl aryl ether
    • 

  • Benzenoid
    • 

  • Heteroaromatic compound
    • 

  • Pyrrole
    • 

  • Carboxamide group
    • 

  • Secondary carboxylic acid amide
    • 

  • Lactam
    • 

  • Carboxylic acid derivative
    • 

  • Ether
    • 

  • Azacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • 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
logP1.37ALOGPS
logP0.95ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)13.91ChemAxon
pKa (Strongest Basic)-1.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area54.12 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity60.77 m³·mol⁻¹ChemAxon
Polarizability22.96 ųChemAxon
Number of Rings3ChemAxon
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 Compound179484  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available