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6a

E3L066654
Internal ID: LIG001224
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG001224/LIG001224.sdf
Basic Properties
Compound ID
E3L066654
Internal ID
LIG001224
Molecular formula
C12H12N2O3
Molecular weight
232.239000
Exact mass
232.084792
XLogP
0.2216
TPSA
75.2700
HBA / HBD
3 / 2
Rotatable bonds
2
Heavy atoms / rings
17 / 2
Activity summary
Kd unknown 20.00000000 nM
7 activity record(s) imported
InChIKey
QDCDITVKCKBZTO-UHFFFAOYSA-N
SMILES
O=C1CCC(NC(=O)c2ccccc2)C(=O)N1
Aliases
6a (preferred) 7 (synonym) 7 (source_name) BDBM631083 (source_id) e3_ligand:102 (source_id) MolGlueDB:900 (source_id) MolGlueDB:900 (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:BDBM631083 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM631083 medium
; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 direct_binder e3_ligand Yes Yes medium e3_ligand:102 high
; deduplicated e3_ligand:102 into MolGlueDB:900; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB900 Open -
e3_ligand 102 Open - 10.1021/acs.jmedchem.3c00851
BindingDB BDBM631083 Open - 10.7270/Q20869GN; 10.7270/Q2FN1BRK; 10.1021/acs.jmedchem.3c00851; 10.7270/Q20K2F7R PMID: 37902300; 38917956
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM631083 BDBM631083 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:102 - exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:900; exact_duplicate; Tanimoto 1.0
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CCC(NC(=O)c2ccccc2)C(=O)N1 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG001224/LIG001224.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG001224/LIG001224.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG001224/LIG001224.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG001224/LIG001224.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG001224/LIG001224.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM631083 Kd 75000 nM Low DOI: 10.7270/Q2FN1BRK 2 source records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM631083 Kd 20 nM High DOI: 10.7270/Q20869GN 2 source records
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM631083 IC50 127000 nM Low DOI: 10.1021/acs.jmedchem.3c00851
PMID: 37902300 		1
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM631083 Ki 63000 nM Low DOI: 10.1021/acs.jmedchem.3c00851
PMID: 37902300 		1
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM631083 Ki 62600 nM Low DOI: 10.7270/Q20K2F7R
PMID: 38917956 		1