< Back to small molecule database

BDBM756558

E3L039559
Internal ID: BDB039559
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB039559/BDB039559.sdf
Basic Properties
Compound ID
E3L039559
Internal ID
BDB039559
Molecular formula
C27H25F2N5O4
Molecular weight
521.524000
Exact mass
521.187461
XLogP
2.4953
TPSA
107.6300
HBA / HBD
6 / 2
Rotatable bonds
3
Heavy atoms / rings
38 / 7
Activity summary
IC50 < 100.00000000 nM
2 activity record(s) imported
InChIKey
VTYXEEHOQCVELO-DQUNLGLBSA-N
SMILES
O=C1CC[C@H](N2Cc3c(ccc4c3OCC43CCN(Cc4cccc5cn[nH]c45)CC3(F)F)C2=O)C(=O)N1
Aliases
BDBM756558 (preferred) (3S)-3-[3',3'-difluoro-1'-(1H-indazol-7-ylmethyl)-6-oxospiro[2,8-dihydrofuro[2,3-e]isoindole-3,4'-piperidine]-7-yl]piperidine-2,6-dione (source_name) BDBM756558 (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:BDBM756558 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM756558 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM756558 Open - 10.7270/Q21V5KQW
PubChem CID169201196 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CC[C@H](N2Cc3c(ccc4c3OCC43CCN(Cc4cccc5cn[nH]c45)CC3(F)F)C2=O)C(=O)N1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB039559/BDB039559.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB039559/BDB039559.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB039559/BDB039559.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB039559/BDB039559.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB039559/BDB039559.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM756558 IC50 <100 nM High DOI: 10.7270/Q21V5KQW 2 source records