< Back to small molecule database

BDBM627132

E3L031342
Internal ID: BDB031342
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB031342/BDB031342.sdf
Basic Properties
Compound ID
E3L031342
Internal ID
BDB031342
Molecular formula
C20H16N4O3
Molecular weight
360.373000
Exact mass
360.122240
XLogP
3.1791
TPSA
99.8700
HBA / HBD
4 / 3
Rotatable bonds
4
Heavy atoms / rings
27 / 4
Activity summary
Kd unknown 109.00000000 nM
2 activity record(s) imported
InChIKey
JZKGVZSLHZXJHU-UHFFFAOYSA-N
SMILES
COc1cccc(-c2ncccc2C(=O)Nc2ccc3[nH]c(=O)[nH]c3c2)c1
Aliases
BDBM627132 (preferred) 2-(3-methoxyphenyl)-N-(2-oxo-1,3-dihydrobenzimidazol-5-yl)pyridine-3-carboxamide (source_name) BDBM627132 (source_id)
E3 Relation
E3 UniProt Gene / protein Relation type Ligand role Direct Functional Docking Source Evidence
Q16531 DDB1;XAP1
DNA damage-binding protein 1		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627132 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627132 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM627132 Open - 10.7270/Q2HD80T6
PubChem CID137525634 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready COc1cccc(-c2ncccc2C(=O)Nc2ccc3[nH]c(=O)[nH]c3c2)c1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB031342/BDB031342.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB031342/BDB031342.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB031342/BDB031342.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB031342/BDB031342.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB031342/BDB031342.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM627132 Kd 109 nM Moderate DOI: 10.7270/Q2HD80T6 2 source records