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BDBM627129

E3L031339
Internal ID: BDB031339
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB031339/BDB031339.sdf
Basic Properties
Compound ID
E3L031339
Internal ID
BDB031339
Molecular formula
C19H20ClN5O2
Molecular weight
385.855000
Exact mass
385.130553
XLogP
2.8593
TPSA
84.2300
HBA / HBD
3 / 3
Rotatable bonds
3
Heavy atoms / rings
27 / 4
Activity summary
Kd unknown 7.00000000 nM
2 activity record(s) imported
InChIKey
RJTYGLBDHCZEDN-UHFFFAOYSA-N
SMILES
O=C(Nc1ccc2[nH]c(=O)[nH]c2c1)N1CCN(Cc2ccc(Cl)cc2)CC1
Aliases
BDBM627129 (preferred) 4-[(4-chlorophenyl)methyl]-N-(2-oxo-1,3-dihydrobenzimidazol-5-yl)piperazine-1-carboxamide (source_name) BDBM627129 (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:BDBM627129 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627129 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM627129 Open - 10.7270/Q2HD80T6
PubChem CID137525789 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C(Nc1ccc2[nH]c(=O)[nH]c2c1)N1CCN(Cc2ccc(Cl)cc2)CC1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB031339/BDB031339.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB031339/BDB031339.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB031339/BDB031339.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB031339/BDB031339.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB031339/BDB031339.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM627129 Kd 7 nM Very high DOI: 10.7270/Q2HD80T6 2 source records