IMPPAT Phytochemical information: 
Palmatine

Palmatine
Summary

SMILES: COc1cc2CC[n+]3c(-c2cc1OC)cc1c(c3)c(OC)c(cc1)OC
InChI: InChI=1S/C21H22NO4/c1-23-18-6-5-13-9-17-15-11-20(25-3)19(24-2)10-14(15)7-8-22(17)12-16(13)21(18)26-4/h5-6,9-12H,7-8H2,1-4H3/q+1
InChIKey: QUCQEUCGKKTEBI-UHFFFAOYSA-N
DeepSMILES: COcccCC[n+]c-c6cc%10OC)))))cccc6)cOC))ccc6))OC
Scaffold Graph/Node/Bond level: c1ccc2c(c1)CC[n+]1cc3ccccc3cc1-2
Scaffold Graph/Node level: C1CCC2CN3CCC4CCCCC4C3CC2C1
Scaffold Graph level: C1CCC2CC3C(CCC4CCCCC43)CC2C1
Functional groups: cOC; c[n+](c)C
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Alkaloids and derivatives
ClassyFire Class: Protoberberine alkaloids and derivatives
Synonymous chemical names:
gindarinine, Palmatine, palmitine, berbericinine, palmatine
External chemical identifiers:
CID:CID_19009; ChEMBL:CHEMBL206106; ChEBI:CHEBI:16096; ZINC:ZINC000000608233; FDASRS:G50C034217; SureChEMBL:SCHEMBL562120; MolPort-002-507-435
Chemical structure download


Palmatine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 352.41
Log P RDKit 3.38
Topological polar surface area (Å2) RDKit 40.8
Number of hydrogen bond acceptors RDKit 4
Number of hydrogen bond donors RDKit 0
Number of carbon atoms RDKit 21
Number of heavy atoms RDKit 26
Number of heteroatoms RDKit 5
Number of nitrogen atoms RDKit 1
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 15
Number of sp3 hybridized carbon atoms RDKit 6
Shape complexity RDKit 0.29
Number of rotatable bonds RDKit 4
Number of aliphatic carbocycles RDKit 0
Number of aliphatic heterocycles RDKit 1
Number of aliphatic rings RDKit 1
Number of aromatic carbocycles RDKit 2
Number of aromatic heterocycles RDKit 1
Number of aromatic rings RDKit 3
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


Palmatine
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 0.675155


Palmatine
ADME properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Moderately soluble
Solubility class [Silicos-IT] SwissADME Poorly soluble
Blood Brain Barrier permeation SwissADME Yes
Gastrointestinal absorption SwissADME High
Log Kp (Skin permeation, cm/s) SwissADME -5.79
Number of PAINS structural alerts SwissADME 0
Number of Brenk structural alerts SwissADME 1
CYP1A2 inhibitor SwissADME No
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME Yes
CYP3A4 inhibitor SwissADME Yes
P-glycoprotein substrate SwissADME Yes


Palmatine
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_000616ENSG00000111700SLCO1B328234ChEMBL, NPASS
TAR_EXP_000450ENSG00000004487KDM1A23028BindingDB, ChEMBL
TAR_EXP_000369ENSG00000100393EP3002033BindingDB, ChEMBL, NPASS
TAR_EXP_000833ENSG00000160789LMNA4000NPASS
TAR_EXP_001663ENSG00000162607USP17398NPASS
TAR_EXP_001343ENSG00000114200BCHE590BindingDB, ChEMBL, NPASS
TAR_EXP_001306ENSG00000196396PTPN15770NPASS
TAR_EXP_000687ENSG00000100644HIF1A3091NPASS
TAR_EXP_001191ENSG00000085377PREP5550NPASS
TAR_EXP_000881ENSG00000087085ACHE43BindingDB, ChEMBL, NPASS
TAR_EXP_000061ENSG00000134538SLCO1B110599ChEMBL, NPASS
TAR_EXP_000280ENSG00000160868CYP3A41576BindingDB
TAR_EXP_000276ENSG00000272532CYP2D61565NPASS
TAR_EXP_000004ENSG00000094631HDAC610013ChEMBL