< Back to small molecule database

BDBM97039

E3L004262
Internal ID: BDB004262
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB004262/BDB004262.sdf
Basic Properties
Compound ID
E3L004262
Internal ID
BDB004262
Molecular formula
C46H50N6O5
Molecular weight
766.943000
Exact mass
766.384269
XLogP
5.6751
TPSA
118.5500
HBA / HBD
9 / 2
Rotatable bonds
7
Heavy atoms / rings
57 / 10
Activity summary
IC50 unknown 275.00000000 nM
2 activity record(s) imported
InChIKey
MOXUHRVGVLTQQM-PQGYCHLWSA-N
SMILES
O=C1CCC(N2Cc3cc(N4CCN(CC5CC6(CCN(c7ccc([C@@H]8c9ccc(O)cc9OC[C@@H]8c8ccccc8)cn7)CC6)C5)CC4)ccc3C2=O)C(=O)N1
Aliases
BDBM97039 (preferred) 3-(5-(4-((7-(5-((3S,4R)-7-hydroxy-3-phenylchroman-4-yl)pyridin-2-yl)-7-azaspiro [3.5]nonan-2-yl)methyl)piperazin-1-yl)-1-oxoisoindolin-2-yl)piperidine-2,6-dione (source_name) BDBM97039 (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:BDBM97039 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM97039 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM97039 Open - 10.7270/Q22F7T7F
PubChem CID170728513 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CCC(N2Cc3cc(N4CCN(CC5CC6(CCN(c7ccc([C@@H]8c9ccc(O)cc9OC[C@@H]8c8ccccc8)cn7)CC6)C5)CC4)ccc3C2=O)C(=O)N1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB004262/BDB004262.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB004262/BDB004262.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB004262/BDB004262.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB004262/BDB004262.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB004262/BDB004262.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM97039 IC50 275 nM Moderate DOI: 10.7270/Q22F7T7F 2 source records