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Berberine

E3L048416
Internal ID: BDB048416
Activity data available Local docking-ready structure
Dock with Q07869 Dock with Q09472
Structure
/e3_file/ligand_db/generated/BDB048416/BDB048416.sdf
Basic Properties
Compound ID
E3L048416
Internal ID
BDB048416
Molecular formula
C20H18NO4+
Molecular weight
336.367000
Exact mass
336.123034
XLogP
3.0963
TPSA
40.8000
HBA / HBD
4 / 0
Rotatable bonds
2
Heavy atoms / rings
25 / 5
Activity summary
EC50 unknown 580.00000000 nM
3 activity record(s) imported
InChIKey
YBHILYKTIRIUTE-UHFFFAOYSA-N
SMILES
COc1ccc2cc3[n+](cc2c1OC)CCc1cc2c(cc1-3)OCO2
Aliases
BDBM50203126 (preferred) Berberine (source_name) BDBM50203126 (source_id)
E3 Relation
E3 UniProt Gene / protein Relation type Ligand role Direct Functional Docking Source Evidence
Q07869 PPARA;NR1C1;PPAR
Peroxisome proliferator-activated receptor alpha		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50203126 medium
; target=Peroxisome proliferator-activated receptor alpha
Q09472 EP300;P300
Histone acetyltransferase p300		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50203126 medium
; target=Histone acetyltransferase p300
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM50203126 Open - 10.7270/Q2988C8B; 10.7270/Q28D01VV PMID: 33992930; 38215590
PubChem CID2353 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready COc1ccc2cc3[n+](cc2c1OC)CCc1cc2c(cc1-3)OCO2 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB048416/BDB048416.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB048416/BDB048416.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB048416/BDB048416.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB048416/BDB048416.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB048416/BDB048416.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
Histone acetyltransferase p300
Q09472
E3 ligase component 		BindingDB:BDBM50203126 IC50 8910 nM Low DOI: 10.7270/Q28D01VV
PMID: 38215590 		1
Peroxisome proliferator-activated receptor alpha
Q07869
E3 ligase component 		BindingDB:BDBM50203126 EC50 580 nM Moderate DOI: 10.7270/Q2988C8B
PMID: 33992930 		1
Peroxisome proliferator-activated receptor alpha
Q07869
E3 ligase component 		BindingDB:BDBM50203126 Ki 730 nM Moderate DOI: 10.7270/Q2988C8B
PMID: 33992930 		1