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25

E3L066205
Internal ID: LIG000775
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG000775/LIG000775.sdf
Basic Properties
Compound ID
E3L066205
Internal ID
LIG000775
Molecular formula
C11H11NO2
Molecular weight
189.214000
Exact mass
189.078979
XLogP
1.2068
TPSA
46.1700
HBA / HBD
2 / 1
Rotatable bonds
1
Heavy atoms / rings
14 / 2
Activity summary
IC50 unknown 2191.00000000 nM
3 activity record(s) imported
InChIKey
KAKZYGLQCHMNGS-UHFFFAOYSA-N
SMILES
O=C1CCC(c2ccccc2)C(=O)N1
Aliases
25 (preferred) 2a(PG) (synonym) 2a(PG) (source_name) PG (source_name) BDBM475151 (source_id) e3_ligand:74 (source_id) MolGlueDB:929 (source_id) MolGlueDB:929 (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:BDBM475151 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM475151 medium
; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 direct_binder e3_ligand Yes Yes medium e3_ligand:74 high
; deduplicated e3_ligand:74 into MolGlueDB:929; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB929 Open -
e3_ligand 74 Open - 10.1002/anie.202108848
BindingDB BDBM475151 Open - 10.7270/Q2P84FZ1; 10.7270/Q2RJ4Q22 PMID: 38889052
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM475151 BDBM475151 exact_full_inchikey no_new_bindingdb_compound_link_evidence_to_base 1.000000
chiral 1.000000 		Exact structure already exists in E3/MolGlue base library
e3_ligand:74 PG exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:929; exact_duplicate; Tanimoto 1.0
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CCC(c2ccccc2)C(=O)N1 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG000775/LIG000775.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG000775/LIG000775.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG000775/LIG000775.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG000775/LIG000775.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG000775/LIG000775.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM475151 Kd 30000 nM Low DOI: 10.7270/Q2P84FZ1 2 source records
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM475151 IC50 2191 nM Low DOI: 10.7270/Q2RJ4Q22
PMID: 38889052 		1