< Back to small molecule database

BDBM627147

E3L031357
Internal ID: BDB031357
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB031357/BDB031357.sdf
Basic Properties
Compound ID
E3L031357
Internal ID
BDB031357
Molecular formula
C14H12N4O3
Molecular weight
284.275000
Exact mass
284.090940
XLogP
1.7814
TPSA
99.8700
HBA / HBD
5 / 3
Rotatable bonds
3
Heavy atoms / rings
21 / 3
Activity summary
Kd unknown 16.00000000 nM
2 activity record(s) imported
InChIKey
ZTUXQDFEKFKSQT-UHFFFAOYSA-N
SMILES
COC(=O)c1ccc(Nc2ccc3[nH]c(=O)[nH]c3c2)nc1
Aliases
BDBM627147 (preferred) Methyl 6-[(2-oxo-1,3-dihydrobenzimidazol-5-yl)amino]pyridine-3-carboxylate (source_name) BDBM627147 (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:BDBM627147 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM627147 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM627147 Open - 10.7270/Q2HD80T6
PubChem CID137526053 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready COC(=O)c1ccc(Nc2ccc3[nH]c(=O)[nH]c3c2)nc1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB031357/BDB031357.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB031357/BDB031357.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB031357/BDB031357.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB031357/BDB031357.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB031357/BDB031357.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM627147 Kd 16 nM High DOI: 10.7270/Q2HD80T6 2 source records