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BDBM627056

E3L031269
Internal ID: BDB031269
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB031269/BDB031269.sdf
Basic Properties
Compound ID
E3L031269
Internal ID
BDB031269
Molecular formula
C13H16N4O2
Molecular weight
260.297000
Exact mass
260.127326
XLogP
0.5247
TPSA
72.2000
HBA / HBD
3 / 2
Rotatable bonds
1
Heavy atoms / rings
19 / 3
Activity summary
Kd < 1.00000000 nM
2 activity record(s) imported
InChIKey
SKOAJHDLYSDNOU-UHFFFAOYSA-N
SMILES
CC(=O)N1CCN(c2ccc3[nH]c(=O)[nH]c3c2)CC1
Aliases
BDBM627056 (preferred) 5-(4-Acetylpiperazin-1-yl)-1,3-dihydrobenzimidazol-2-one (source_name) BDBM627056 (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:BDBM627056 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627056 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM627056 Open - 10.7270/Q2HD80T6
PubChem CID110642420 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready CC(=O)N1CCN(c2ccc3[nH]c(=O)[nH]c3c2)CC1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB031269/BDB031269.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB031269/BDB031269.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB031269/BDB031269.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB031269/BDB031269.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB031269/BDB031269.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM627056 Kd <1 nM Very high DOI: 10.7270/Q2HD80T6 2 source records