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BDBM557644

E3L026391
Internal ID: BDB026391
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB026391/BDB026391.sdf
Basic Properties
Compound ID
E3L026391
Internal ID
BDB026391
Molecular formula
C15H17N5O4
Molecular weight
331.332000
Exact mass
331.128054
XLogP
-0.5140
TPSA
128.2200
HBA / HBD
4 / 3
Rotatable bonds
3
Heavy atoms / rings
24 / 3
Activity summary
IC50 < 1000.00000000 nM
2 activity record(s) imported
InChIKey
JWWNHZKTSXKZFK-UHFFFAOYSA-N
SMILES
Cn1c(=O)n(C2CCC(=O)NC2=O)c2ccc(CNC(N)=O)cc21
Aliases
BDBM557644 (preferred) [1-(2,6-Dioxopiperidin-3-yl)-3-methyl-2-oxobenzimidazol-5-yl]methylurea (source_name) BDBM557644 (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:BDBM557644 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM557644 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM557644 Open - 10.7270/Q23T9MFH
PubChem CID138491609 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready Cn1c(=O)n(C2CCC(=O)NC2=O)c2ccc(CNC(N)=O)cc21 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB026391/BDB026391.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB026391/BDB026391.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB026391/BDB026391.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB026391/BDB026391.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB026391/BDB026391.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM557644 IC50 <1000 nM Uncertain DOI: 10.7270/Q23T9MFH 2 source records