IMPPAT Phytochemical information: 
Harmalacidine

Harmalacidine
Summary

SMILES: COc1ccc2c(c1)[nH]c1c2CCNC1=O
InChI: 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)
InChIKey: MWEGNYFSTKOOSD-UHFFFAOYSA-N
DeepSMILES: COcccccc6)[nH]cc5CCNC6=O
Scaffold Graph/Node/Bond level: O=C1NCCc2c1[nH]c1ccccc21
Scaffold Graph/Node level: OC1NCCC2C3CCCCC3NC12
Scaffold Graph level: CC1CCCC2C1CC1CCCCC12
Functional groups: cOC; c[nH]c; cC(=O)NC
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Organoheterocyclic compounds
ClassyFire Class: Indoles and derivatives
ClassyFire Subclass: Pyridoindoles
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Tryptophan alkaloids
NP Classifier Class: Carboline alkaloids
Synonymous chemical names:
harmalacidine
External chemical identifiers:
CID:CID_179484; ChEMBL:CHEMBL4059776; SureChEMBL:SCHEMBL1520427
Chemical structure download


Harmalacidine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 216.24
Log P RDKit 1.46
Topological polar surface area (Å2) RDKit 54.12
Number of hydrogen bond acceptors RDKit 2
Number of hydrogen bond donors RDKit 2
Number of carbon atoms RDKit 12
Number of heavy atoms RDKit 16
Number of heteroatoms RDKit 4
Number of nitrogen atoms RDKit 2
Number of sulfur atoms RDKit 0
Number of chiral carbon atoms RDKit 0
Stereochemical complexity RDKit 0
Number of sp hybridized carbon atoms RDKit 0
Number of sp2 hybridized carbon atoms RDKit 9
Number of sp3 hybridized carbon atoms RDKit 3
Shape complexity RDKit 0.25
Number of rotatable bonds RDKit 0
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 1
Number of aliphatic rings RDKit 1
Number of aromatic carbocycles RDKit 1
Number of aromatic heterocycles RDKit 1
Number of aromatic rings RDKit 2
Total number of rings RDKit 3
Number of saturated carbocycles RDKit 0
Number of saturated heterocycles RDKit 0
Number of saturated rings RDKit 0
Number of Smallest Set of Smallest Rings (SSSR) RDKit 3


Harmalacidine
Drug-likeness properties
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 0
Lipinski’s rule of 5 RDKit Passed
Number of Ghose rule violations RDKit 0
Ghose rule RDKit Passed
Veber rule RDKit Good
Egan rule RDKit Good
GSK 4/400 rule RDKit Good
Pfizer 3/75 rule RDKit Bad
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.76


Harmalacidine
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Soluble
Solubility class [Silicos-IT] SwissADME Moderately soluble
Blood Brain Barrier permeation SwissADME Yes
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -6.44
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 0
CYP1A2 inhibitor SwissADME Yes
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME No
CYP3A4 inhibitor SwissADME No
P-glycoprotein substrate SwissADME Yes