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5-Pyridin-3-yl-1,3-dihydrobenzimidazol-2-one

E3L031227
Internal ID: BDB031227
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB031227/BDB031227.sdf
Basic Properties
Compound ID
E3L031227
Internal ID
BDB031227
Molecular formula
C12H9N3O
Molecular weight
211.224000
Exact mass
211.074562
XLogP
1.9182
TPSA
61.5400
HBA / HBD
2 / 2
Rotatable bonds
1
Heavy atoms / rings
16 / 3
Activity summary
Kd unknown 7.00000000 nM
2 activity record(s) imported
InChIKey
ZRTKTZIAVVSSAA-UHFFFAOYSA-N
SMILES
O=c1[nH]c2ccc(-c3cccnc3)cc2[nH]1
Aliases
BDBM627013 (preferred) 5-Pyridin-3-yl-1,3-dihydrobenzimidazol-2-one (source_name) BDBM627013 (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:BDBM627013 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627013 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM627013 Open - 10.7270/Q2HD80T6
PubChem CID20535851 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=c1[nH]c2ccc(-c3cccnc3)cc2[nH]1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB031227/BDB031227.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB031227/BDB031227.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB031227/BDB031227.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB031227/BDB031227.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB031227/BDB031227.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM627013 Kd 7 nM Very high DOI: 10.7270/Q2HD80T6 2 source records