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BDBM627127

E3L031337
Internal ID: BDB031337
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB031337/BDB031337.sdf
Basic Properties
Compound ID
E3L031337
Internal ID
BDB031337
Molecular formula
C15H13N5O3
Molecular weight
311.301000
Exact mass
311.101839
XLogP
0.8631
TPSA
119.7400
HBA / HBD
4 / 4
Rotatable bonds
3
Heavy atoms / rings
23 / 3
Activity summary
Kd unknown 121.00000000 nM
2 activity record(s) imported
InChIKey
KRCKXXZEQLFLHI-UHFFFAOYSA-N
SMILES
CNC(=O)c1ccc(C(=O)Nc2ccc3[nH]c(=O)[nH]c3c2)cn1
Aliases
BDBM627127 (preferred) 2-N-methyl-5-N-(2-oxo-1,3-dihydrobenzimidazol-5-yl)pyridine-2,5-dicarboxamide (source_name) BDBM627127 (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:BDBM627127 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627127 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM627127 Open - 10.7270/Q2HD80T6
PubChem CID137525584 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready CNC(=O)c1ccc(C(=O)Nc2ccc3[nH]c(=O)[nH]c3c2)cn1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB031337/BDB031337.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB031337/BDB031337.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB031337/BDB031337.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB031337/BDB031337.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB031337/BDB031337.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM627127 Kd 121 nM Moderate DOI: 10.7270/Q2HD80T6 2 source records