IMPPAT Phytochemical information: 
Berberine
Berberine
Summary

SMILES: COc1c(OC)ccc2c1c[n+]1CCc3c(-c1c2)cc1c(c3)OCO1
InChI: InChI=1S/C20H18NO4/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2/h3-4,7-10H,5-6,11H2,1-2H3/q+1
InChIKey: YBHILYKTIRIUTE-UHFFFAOYSA-N
DeepSMILES: COccOC))cccc6c[n+]CCcc-c6c%10))cccc6)OCO5
Scaffold Graph/Node/Bond level: c1ccc2c[n+]3c(cc2c1)-c1cc2c(cc1CC3)OCO2
Scaffold Graph/Node level: C1CCC2CN3CCC4CC5OCOC5CC4C3CC2C1
Scaffold Graph level: C1CCC2CC3C(CCC4CC5CCCC5CC43)CC2C1
Functional groups: c1cOCO1; cOC; c[n+](c)C
Chemical classification
ClassyFire Kingdom: Organic compounds
ClassyFire Superclass: Alkaloids and derivatives
ClassyFire Class: Protoberberine alkaloids and derivatives
NP Classifier Biosynthetic pathway: Alkaloids
NP Classifier Superclass: Tyrosine alkaloids
NP Classifier Class: Protoberberine alkaloids|Isoquinoline alkaloids
Synonymous chemical names:
berbericine, berberine, umbellatine
External chemical identifiers:
CID:2353; ChEMBL:CHEMBL295124; ChEBI:16118; ZINC:ZINC000003779067; FDASRS:0I8Y3P32UF; SureChEMBL:SCHEMBL25632; MolPort-002-507-191
Chemical structure download
2D:2D MOL2D MOL22D SDF
3D:3D MOL3D MOL23D SDF3D PDB3D PDBQT
Berberine
Physicochemical properties
Property name Tool Property value
Molecular weight (g/mol) RDKit 0
Log P RDKit 0
Topological polar surface area (Å2) RDKit
Number of hydrogen bond acceptors RDKit
Number of hydrogen bond donors RDKit
Number of carbon atoms RDKit
Number of heavy atoms RDKit
Number of heteroatoms RDKit
Number of nitrogen atoms RDKit
Number of sulfur atoms RDKit
Number of chiral carbon atoms RDKit
Stereochemical complexity RDKit 0
Number of sp hybridized carbon atoms RDKit
Number of sp2 hybridized carbon atoms RDKit
Number of sp3 hybridized carbon atoms RDKit
Shape complexity RDKit
Number of rotatable bonds RDKit
Number of aliphatic carbocycles RDKit
Number of aliphatic heterocycles RDKit
Number of aliphatic rings RDKit
Number of aromatic carbocycles RDKit
Number of aromatic heterocycles RDKit
Number of aromatic rings RDKit
Total number of rings RDKit
Number of saturated carbocycles RDKit
Number of saturated heterocycles RDKit
Number of saturated rings RDKit
Number of Smallest Set of Smallest Rings (SSSR) RDKit
Berberine
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 0.6745
Berberine
ADMET properties
Property nameToolProperty value
Bioavailability score SwissADME 0.55
Solubility class [ESOL] SwissADME Moderately 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 -5.78
Number of PAINS structural alerts SwissADME 0.0
Number of Brenk structural alerts SwissADME 1.0
CYP1A2 inhibitor SwissADME Yes
CYP2C19 inhibitor SwissADME No
CYP2C9 inhibitor SwissADME No
CYP2D6 inhibitor SwissADME Yes
CYP3A4 inhibitor SwissADME Yes
P-glycoprotein substrate SwissADME Yes
Berberine
Predicted human target proteins
Protein identifierHGNC symbolCombined score from STITCH database
ENSP00000013034NME1800
ENSP00000155840KCNQ1800
ENSP00000215832MAPK1897
ENSP00000216117HMOX1841
ENSP00000219070MMP2733
ENSP00000222381PON1800
ENSP00000223190NRF1800
ENSP00000227507CCND1841
ENSP00000242057AHR700
ENSP00000261707SLC6A4800
ENSP00000262291VMP1800
ENSP00000264657STAT3835
ENSP00000266000DAXX810
ENSP00000269305TP53863
ENSP00000270202AKT1948
ENSP00000275493EGFR800
ENSP00000285930AKR1B1800
ENSP00000287139NODAL800
ENSP00000287295AIFM1800
ENSP00000302846PTGER4820
ENSP00000303208PCSK9853
ENSP00000303830INSR818
ENSP00000309572TERT700
ENSP00000309757LPL800
ENSP00000311032CASP3947
ENSP00000312029UCP2818
ENSP00000312286PLA2G1B794
ENSP00000312987HNF4A732
ENSP00000312988NFKBIB786
ENSP00000320709ADIPOQ824
ENSP00000320935SLC2A4828
ENSP00000324806GSK3B700
ENSP00000324856STK11825
ENSP00000327251NOS2786
ENSP00000330237CASP9700
ENSP00000342070CTSB823
ENSP00000344192IL17A800
ENSP00000345681GATA2800
ENSP00000346839FN1800
ENSP00000348170HP836
ENSP00000350941SRC800
ENSP00000351273CASP8700
ENSP00000353731DPP4841
ENSP00000353820CYP2D6816
ENSP00000354522TOP1768
ENSP00000355231BECN1800
ENSP00000355759PARP1749
ENSP00000356438PTGS2829
ENSP00000360266JUN822
ENSP00000360683PTPN1800
ENSP00000361405MMP9822
ENSP00000361850PLAU800
ENSP00000363089TLR4800
ENSP00000369050CYP1A1700
ENSP00000369757RPS6700
ENSP00000376127MAU2800
ENSP00000377878ATP5G2841
ENSP00000379701HNF4G732
ENSP00000387123ALDH7A1800
ENSP00000387662GCG814
ENSP00000398698TNF757
ENSP00000424038CASP12800
ENSP00000441691ITGAM822
ENSP00000441828HPR836
ENSP00000454071LDLR855
The human target proteins were predicted using STITCH, a database of Chemical-Protein interaction networks.