< Back to small molecule database

BDBM575281

E3L027956
Internal ID: BDB027956
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB027956/BDB027956.sdf
Basic Properties
Compound ID
E3L027956
Internal ID
BDB027956
Molecular formula
C13H14N4O2
Molecular weight
258.281000
Exact mass
258.111676
XLogP
0.7904
TPSA
76.0200
HBA / HBD
4 / 2
Rotatable bonds
2
Heavy atoms / rings
19 / 3
Activity summary
Kd unknown 30000.00000000 nM
4 activity record(s) imported
InChIKey
IKIYACAMAWJHJP-UHFFFAOYSA-N
SMILES
Cn1cnc2cc(NC3CCC(=O)NC3=O)ccc21
Aliases
BDBM575281 (preferred) 3-[(1-Methylbenzimidazol-5-yl)amino]piperidine-2,6-dione (source_name) BDBM575281 (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:BDBM575281 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM575281 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM575281 Open - 10.7270/Q2H1357Z; 10.7270/Q20869F6
PubChem CID146573416 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready Cn1cnc2cc(NC3CCC(=O)NC3=O)ccc21 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB027956/BDB027956.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB027956/BDB027956.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB027956/BDB027956.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB027956/BDB027956.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB027956/BDB027956.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM575281 Kd 30000 nM Low DOI: 10.7270/Q2H1357Z 2 source records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM575281 Kd 30000 nM Low DOI: 10.7270/Q20869F6 2 source records