IMPPAT Phytochemical information: 
Harmaline

Harmaline
Summary

SMILES: COc1ccc2c(c1)[nH]c1c2CCN=C1C
InChI: InChI=1S/C13H14N2O/c1-8-13-11(5-6-14-8)10-4-3-9(16-2)7-12(10)15-13/h3-4,7,15H,5-6H2,1-2H3
InChIKey: RERZNCLIYCABFS-UHFFFAOYSA-N
DeepSMILES: COcccccc6)[nH]cc5CCN=C6C
Scaffold Graph/Node/Bond level: C1=NCCc2c1[nH]c1ccccc21
Scaffold Graph/Node level: C1CCC2C(C1)NC1CNCCC12
Scaffold Graph level: C1CCC2C(C1)CC1CCCCC12
Functional groups: c[nH]c; cOC; cC(C)=NC
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Alkaloids and derivatives
ClassyFire Class: Harmala alkaloids
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Tryptophan alkaloids
NP Classifier Class: Carboline alkaloids
Synonymous chemical names:
harmaline, harmidine, Harmaline, Harmidine
External chemical identifiers:
CID:CID_3564; ChEMBL:CHEMBL340807; ChEBI:CHEBI:28172; ZINC:ZINC000100014157; FDASRS:CN58I4TOET; SureChEMBL:SCHEMBL199260
Chemical structure download


Harmaline
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 214.27
Log P RDKit 2.54
Topological polar surface area (Å2) RDKit 37.38
Number of hydrogen bond acceptors RDKit 2
Number of hydrogen bond donors RDKit 1
Number of carbon atoms RDKit 13
Number of heavy atoms RDKit 16
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 4
Shape complexity RDKit 0.31
Number of rotatable bonds RDKit 1
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


Harmaline
Drug-likeness
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 0.77784


Harmaline
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 -6.14
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 Yes
CYP3A4 inhibitor SwissADME No
P-glycoprotein substrate SwissADME Yes


Harmaline
Phytochemical - Human target proteins supported by experimental evidence associations
Human target proteins supported by experimental evidence
IMPPAT target identifierGene identifierHGNC symbolEntrez Gene identifierSource
TAR_EXP_001861ENSG00000291428BRSK29024ChEMBL
TAR_EXP_001885ENSG00000178999AURKB9212ChEMBL
TAR_EXP_001887ENSG00000100784RPS6KA59252ChEMBL
TAR_EXP_000676ENSG00000072506HSD17B103028ChEMBL
TAR_EXP_001772ENSG00000143479DYRK38444ChEMBL
TAR_EXP_001793ENSG00000134072CAMK18536ChEMBL
TAR_EXP_001775ENSG00000127334DYRK28445ChEMBL
TAR_EXP_001844ENSG00000133101CCNA18900ChEMBL
TAR_EXP_000671ENSG00000103319EEF2K29904ChEMBL
TAR_EXP_001931ENSG00000165304MELK9833ChEMBL
TAR_EXP_000683ENSG00000197386HTT3064ChEMBL
TAR_EXP_000737ENSG00000157219HTR5A3361ChEMBL
TAR_EXP_000735ENSG00000166736HTR3A3359ChEMBL
TAR_EXP_000734ENSG00000147246HTR2C3358ChEMBL
TAR_EXP_000732ENSG00000102468HTR2A3356ChEMBL
TAR_EXP_001796ENSG00000089022MAPKAPK58550ChEMBL
TAR_EXP_001801ENSG00000079277MKNK18569ChEMBL
TAR_EXP_001843ENSG00000145386CCNA2890ChEMBL
TAR_EXP_001911ENSG00000134318ROCK29475ChEMBL
TAR_EXP_000727ENSG00000178394HTR1A3350ChEMBL
TAR_EXP_000728ENSG00000135312HTR1B3351ChEMBL
TAR_EXP_000729ENSG00000179546HTR1D3352ChEMBL
TAR_EXP_001889ENSG00000162889MAPKAPK29261ChEMBL
TAR_EXP_001768ENSG00000004660CAMKK184254ChEMBL
TAR_EXP_000852ENSG00000069535MAOB4129ChEMBL
TAR_EXP_000660ENSG00000082701GSK3B2932ChEMBL
TAR_EXP_001240ENSG00000169032MAP2K15604ChEMBL
TAR_EXP_001286ENSG00000101349PAK557144ChEMBL
TAR_EXP_001360ENSG00000004700RECQL5965ChEMBL
TAR_EXP_001429ENSG00000281877RPS6KA16195ChEMBL
TAR_EXP_000634ENSG00000099875MKNK22872ChEMBL
TAR_EXP_000616ENSG00000111700SLCO1B328234ChEMBL
TAR_EXP_001559ENSG00000096063SRPK16732ChEMBL
TAR_EXP_000554ENSG00000101347SAMHD125939ChEMBL
TAR_EXP_000534ENSG00000182256GABRG32567ChEMBL
TAR_EXP_000533ENSG00000113327GABRG22566ChEMBL
TAR_EXP_000532ENSG00000163285GABRG12565ChEMBL
TAR_EXP_000531ENSG00000102287GABRE2564ChEMBL
TAR_EXP_001431ENSG00000177189RPS6KA36197ChEMBL
TAR_EXP_001492ENSG00000118515SGK16446ChEMBL
TAR_EXP_000535ENSG00000094755GABRP2568ChEMBL
TAR_EXP_001572ENSG00000104375STK36788ChEMBL
TAR_EXP_000530ENSG00000187730GABRD2563ChEMBL
TAR_EXP_000738ENSG00000158748HTR63362ChEMBL
TAR_EXP_000636ENSG00000064393HIPK228996ChEMBL
TAR_EXP_000526ENSG00000145863GABRA62559ChEMBL
TAR_EXP_000527ENSG00000163288GABRB12560ChEMBL
TAR_EXP_001227ENSG00000067606PRKCZ5590ChEMBL
TAR_EXP_001230ENSG00000100030MAPK15594ChEMBL
TAR_EXP_001231ENSG00000102882MAPK35595ChEMBL
TAR_EXP_001710ENSG00000114738MAPKAPK37867ChEMBL
TAR_EXP_001578ENSG00000105146AURKC6795ChEMBL
TAR_EXP_001235ENSG00000107643MAPK85599ChEMBL
TAR_EXP_000528ENSG00000145864GABRB22561ChEMBL
TAR_EXP_000529ENSG00000166206GABRB32562ChEMBL
TAR_EXP_001236ENSG00000185386MAPK115600ChEMBL
TAR_EXP_001237ENSG00000050748MAPK95601ChEMBL
TAR_EXP_001238ENSG00000109339MAPK105602ChEMBL
TAR_EXP_001239ENSG00000156711MAPK135603ChEMBL
TAR_EXP_001728ENSG00000176208ATAD579915ChEMBL
TAR_EXP_000739ENSG00000148680HTR73363ChEMBL
TAR_EXP_000067BUB1B-PAK6106821730ChEMBL
TAR_EXP_000232ENSG00000070770CSNK2A21459ChEMBL
TAR_EXP_001225ENSG00000268089GABRQ55879ChEMBL
TAR_EXP_000101ENSG00000102096PIM211040ChEMBL
TAR_EXP_000107ENSG00000149554CHEK11111ChEMBL
TAR_EXP_000118ENSG00000183765CHEK211200ChEMBL
TAR_EXP_000215ENSG00000151414NEK7140609ChEMBL
TAR_EXP_000222ENSG00000112062MAPK141432ChEMBL
TAR_EXP_000225ENSG00000103653CSK1445ChEMBL
TAR_EXP_000227ENSG00000141551CSNK1D1453ChEMBL
TAR_EXP_000755ENSG00000104365IKBKB3551ChEMBL
TAR_EXP_000231ENSG00000101266CSNK2A11457ChEMBL
TAR_EXP_000276ENSG00000272532CYP2D61565ChEMBL
TAR_EXP_000331ENSG00000157540DYRK1A1859ChEMBL
TAR_EXP_000390ENSG00000142208AKT1207ChEMBL
TAR_EXP_000393ENSG00000105221AKT2208ChEMBL
TAR_EXP_000437ENSG00000274205MAPK15225689ChEMBL
TAR_EXP_000521ENSG00000022355GABRA12554ChEMBL
TAR_EXP_000522ENSG00000151834GABRA22555ChEMBL
TAR_EXP_000523ENSG00000011677GABRA32556ChEMBL
TAR_EXP_000234ENSG00000230700CSNK2B1460ChEMBL
TAR_EXP_001223ENSG00000184304PRKD15587ChEMBL
TAR_EXP_001220ENSG00000065243PKN25586ChEMBL
TAR_EXP_000078ENSG00000119408NEK610783ChEMBL
TAR_EXP_000023ENSG00000110422HIPK310114ChEMBL
TAR_EXP_000027ENSG00000123374CDK21017ChEMBL
TAR_EXP_000032ENSG00000164885CDK51020ChEMBL
TAR_EXP_000855ENSG00000075413MARK34140ChEMBL
TAR_EXP_000858ENSG00000198355PIM3415116ChEMBL
TAR_EXP_000881ENSG00000087085ACHE43ChEMBL
TAR_EXP_000920ENSG00000065534MYLK4638ChEMBL
TAR_EXP_000959ENSG00000117650NEK24751ChEMBL
TAR_EXP_001087ENSG00000140992PDPK15170ChEMBL
TAR_EXP_001119ENSG00000137193PIM15292ChEMBL
TAR_EXP_001139ENSG00000166851PLK15347ChEMBL
TAR_EXP_000851ENSG00000189221MAOA4128ChEMBL
TAR_EXP_001198ENSG00000288516PRKACA5566ChEMBL
TAR_EXP_001206ENSG00000042088TDP155775ChEMBL
TAR_EXP_001207ENSG00000154229PRKCA5578ChEMBL
TAR_EXP_000042ENSG00000130669PAK410298ChEMBL
TAR_EXP_000061ENSG00000134538SLCO1B110599ChEMBL
TAR_EXP_000064ENSG00000110931CAMKK210645ChEMBL
TAR_EXP_001432ENSG00000108443RPS6KB16198ChEMBL
TAR_EXP_000524ENSG00000109158GABRA42557ChEMBL
TAR_EXP_000525ENSG00000186297GABRA52558ChEMBL
TAR_EXP_001467ENSG00000188130MAPK126300ChEMBL