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BDBM756012

E3L039478
Internal ID: BDB039478
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB039478/BDB039478.sdf
Basic Properties
Compound ID
E3L039478
Internal ID
BDB039478
Molecular formula
C28H30N6O3
Molecular weight
498.587000
Exact mass
498.237939
XLogP
2.7196
TPSA
98.7400
HBA / HBD
7 / 1
Rotatable bonds
5
Heavy atoms / rings
37 / 6
Activity summary
IC50 > 5000.00000000 nM
2 activity record(s) imported
InChIKey
PSVXVLXUPOQTTK-UHFFFAOYSA-N
SMILES
CN(C)c1ccnc2c(CN3CCCC3)cc(-c3ccc4c(c3)CN(C3CCC(=O)NC3=O)C4=O)nc12
Aliases
BDBM756012 (preferred) 3-(5-(8-(Dimethylamino)-4-(pyrrolidin-1-ylmethyl)-1,5-naphthyridin-2-yl)-1-oxoisoindolin-2-yl)piperidine-2,6-dione (source_name) BDBM756012 (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:BDBM756012 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM756012 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM756012 Open - 10.7270/Q2WM1K1R
PubChem CID169206313 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready CN(C)c1ccnc2c(CN3CCCC3)cc(-c3ccc4c(c3)CN(C3CCC(=O)NC3=O)C4=O)nc12 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB039478/BDB039478.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB039478/BDB039478.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB039478/BDB039478.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB039478/BDB039478.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB039478/BDB039478.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM756012 IC50 >5000 nM Low DOI: 10.7270/Q2WM1K1R 2 source records