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1-(2-Oxo-1,3-dihydrobenzimidazol-5-yl)-3-phenylurea

E3L031294
Internal ID: BDB031294
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB031294/BDB031294.sdf
Basic Properties
Compound ID
E3L031294
Internal ID
BDB031294
Molecular formula
C14H12N4O2
Molecular weight
268.276000
Exact mass
268.096026
XLogP
2.5002
TPSA
89.7800
HBA / HBD
2 / 4
Rotatable bonds
2
Heavy atoms / rings
20 / 3
Activity summary
Kd unknown 17.00000000 nM
2 activity record(s) imported
InChIKey
ALFSIBQHCVWJSH-UHFFFAOYSA-N
SMILES
O=C(Nc1ccccc1)Nc1ccc2[nH]c(=O)[nH]c2c1
Aliases
BDBM627082 (preferred) 1-(2-Oxo-1,3-dihydrobenzimidazol-5-yl)-3-phenylurea (source_name) BDBM627082 (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:BDBM627082 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627082 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM627082 Open - 10.7270/Q2HD80T6
PubChem CID2326016 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C(Nc1ccccc1)Nc1ccc2[nH]c(=O)[nH]c2c1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB031294/BDB031294.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB031294/BDB031294.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB031294/BDB031294.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB031294/BDB031294.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB031294/BDB031294.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM627082 Kd 17 nM High DOI: 10.7270/Q2HD80T6 2 source records