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BDBM557653

E3L026397
Internal ID: BDB026397
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB026397/BDB026397.sdf
Basic Properties
Compound ID
E3L026397
Internal ID
BDB026397
Molecular formula
C17H17N5O3
Molecular weight
339.355000
Exact mass
339.133139
XLogP
1.0162
TPSA
101.7800
HBA / HBD
4 / 2
Rotatable bonds
2
Heavy atoms / rings
25 / 4
Activity summary
IC50 < 1000.00000000 nM
2 activity record(s) imported
InChIKey
BHVDYWNLSJQLID-UHFFFAOYSA-N
SMILES
Cc1nc(-c2ccc3c(c2)n(C)c(=O)n3C2CCC(=O)NC2=O)c[nH]1
Aliases
BDBM557653 (preferred) 3-[3-methyl-5-(2-methyl-1H-imidazol-5-yl)-2-oxobenzimidazol-1-yl]piperidine-2,6-dione (source_name) BDBM557653 (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:BDBM557653 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM557653 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM557653 Open - 10.7270/Q23T9MFH
PubChem CID138491641 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready Cc1nc(-c2ccc3c(c2)n(C)c(=O)n3C2CCC(=O)NC2=O)c[nH]1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB026397/BDB026397.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB026397/BDB026397.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB026397/BDB026397.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB026397/BDB026397.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB026397/BDB026397.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM557653 IC50 <1000 nM Uncertain DOI: 10.7270/Q23T9MFH 2 source records