IMPPAT Phytochemical information: 
Harmalidine

Harmalidine
Summary

SMILES: COc1ccc2c(c1)n1CC(C3=NCCc2c13)(C)C
InChI: InChI=1S/C16H18N2O/c1-16(2)9-18-13-8-10(19-3)4-5-11(13)12-6-7-17-15(16)14(12)18/h4-5,8H,6-7,9H2,1-3H3
InChIKey: CTEKBWZEYYSNFV-UHFFFAOYSA-N
DeepSMILES: COcccccc6)nCCC=NCCc%10c96))))))C)C
Scaffold Graph/Node/Bond level: c1ccc2c(c1)c1c3n2CCC3=NCC1
Scaffold Graph/Node level: C1CCC2C(C1)C1CCNC3CCN2C31
Scaffold Graph level: C1CCC2C(C1)C1CCCC3CCC2C31
Functional groups: cn(c)C; cOC; cC(=NC)C
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:
harmalidine
External chemical identifiers:
CID:CID_13819666; ZINC:ZINC000015267437; MolPort-035-705-631
Chemical structure download


Harmalidine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 254.33
Log P RDKit 3.03
Topological polar surface area (Å2) RDKit 26.52
Number of hydrogen bond acceptors RDKit 3
Number of hydrogen bond donors RDKit 0
Number of carbon atoms RDKit 16
Number of heavy atoms RDKit 19
Number of heteroatoms RDKit 3
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 7
Shape complexity RDKit 0.44
Number of rotatable bonds RDKit 1
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 2
Number of aliphatic rings RDKit 2
Number of aromatic carbocycles RDKit 1
Number of aromatic heterocycles RDKit 1
Number of aromatic rings RDKit 2
Total number of rings RDKit 4
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 4


Harmalidine
Drug-likeness properties
Property nameToolProperty value
Number of Lipinski’s rule of 5 violations RDKit 0
Lipinski’s rule of 5 filter RDKit Passed
Number of Ghose filter violations RDKit 0
Ghose filter RDKit Passed
Veber filter RDKit Good
Pfizer 3/75 filter RDKit Bad
GSK 4/400 filter RDKit Good
Weighted quantitative estimate of drug-likeness (QEDw) score RDKit 0.767986


Harmalidine
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 -6.01
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 0
CYP1A2 inhibitor SwissADME Yes
CYP2C19 inhibitor SwissADME Yes
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME Yes
CYP3A4 inhibitor SwissADME No
P-glycoprotein substrate SwissADME Yes