< Back to small molecule database

BDBM755997

E3L039465
Internal ID: BDB039465
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB039465/BDB039465.sdf
Basic Properties
Compound ID
E3L039465
Internal ID
BDB039465
Molecular formula
C27H29N5O4
Molecular weight
487.560000
Exact mass
487.221954
XLogP
2.0524
TPSA
107.7700
HBA / HBD
6 / 2
Rotatable bonds
6
Heavy atoms / rings
36 / 6
Activity summary
IC50 > 5000.00000000 nM
2 activity record(s) imported
InChIKey
PVWUDRLADDLBHL-UHFFFAOYSA-N
SMILES
O=C1CCC(N2Cc3cc(-c4cc(CN5CCCC5)c5ccn(CCO)c5n4)ccc3C2=O)C(=O)N1
Aliases
BDBM755997 (preferred) 3-(5-(1-(2-hydroxyethyl)-4-(pyrrolidin-1-ylmethyl)-1H-pyrrolo[2,3-b]pyridin-6-yl)-1-oxoisoindolin-2-yl)piperidine-2,6-dione (source_name) BDBM755997 (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:BDBM755997 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM755997 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM755997 Open - 10.7270/Q2WM1K1R
PubChem CID169206419 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CCC(N2Cc3cc(-c4cc(CN5CCCC5)c5ccn(CCO)c5n4)ccc3C2=O)C(=O)N1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB039465/BDB039465.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB039465/BDB039465.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB039465/BDB039465.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB039465/BDB039465.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB039465/BDB039465.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM755997 IC50 >5000 nM Low DOI: 10.7270/Q2WM1K1R 2 source records