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1-Benzyl-3-(2-oxo-1,3-dihydrobenzimidazol-5-yl)urea

E3L031300
Internal ID: BDB031300
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB031300/BDB031300.sdf
Basic Properties
Compound ID
E3L031300
Internal ID
BDB031300
Molecular formula
C15H14N4O2
Molecular weight
282.303000
Exact mass
282.111676
XLogP
2.1779
TPSA
89.7800
HBA / HBD
2 / 4
Rotatable bonds
3
Heavy atoms / rings
21 / 3
Activity summary
Kd < 1.00000000 nM
2 activity record(s) imported
InChIKey
MMPAEKZDLDYJHX-UHFFFAOYSA-N
SMILES
O=C(NCc1ccccc1)Nc1ccc2[nH]c(=O)[nH]c2c1
Aliases
BDBM627088 (preferred) 1-Benzyl-3-(2-oxo-1,3-dihydrobenzimidazol-5-yl)urea (source_name) BDBM627088 (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:BDBM627088 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627088 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM627088 Open - 10.7270/Q2HD80T6
PubChem CID110748252 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C(NCc1ccccc1)Nc1ccc2[nH]c(=O)[nH]c2c1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB031300/BDB031300.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB031300/BDB031300.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB031300/BDB031300.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB031300/BDB031300.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB031300/BDB031300.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM627088 Kd <1 nM Very high DOI: 10.7270/Q2HD80T6 2 source records