< Back to small molecule database

BDBM97054

E3L004277
Internal ID: BDB004277
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB004277/BDB004277.sdf
Basic Properties
Compound ID
E3L004277
Internal ID
BDB004277
Molecular formula
C44H49N5O4
Molecular weight
711.907000
Exact mass
711.378455
XLogP
6.9654
TPSA
88.5900
HBA / HBD
7 / 2
Rotatable bonds
7
Heavy atoms / rings
53 / 9
Activity summary
IC50 > 5000.00000000 nM
2 activity record(s) imported
InChIKey
OIYBINNRJUPUDP-OLBRMRTOSA-N
SMILES
O=C1CCN(c2ccc(N3CCN(CC4CC5(CCN(c6ccc([C@@H]7c8ccc(O)cc8OC[C@@H]7c7ccccc7)cc6)CC5)C4)CC3)cc2)C(=O)N1
Aliases
BDBM97054 (preferred) 1-(4-(4-((7-(4-((3S,4R)-7-hydroxy-3-phenylchroman-4-yl)phenyl)-7-azaspiro[3.5]nonan-2-yl)methyl)piperazin-1-yl)phenyl)dihydropyrimidine-2,4(1H,3H)-dione (source_name) BDBM97054 (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:BDBM97054 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM97054 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM97054 Open - 10.7270/Q22F7T7F
PubChem CID170728433 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CCN(c2ccc(N3CCN(CC4CC5(CCN(c6ccc([C@@H]7c8ccc(O)cc8OC[C@@H]7c7ccccc7)cc6)CC5)C4)CC3)cc2)C(=O)N1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB004277/BDB004277.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB004277/BDB004277.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB004277/BDB004277.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB004277/BDB004277.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB004277/BDB004277.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM97054 IC50 >5000 nM Low DOI: 10.7270/Q22F7T7F 2 source records