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H_EM12

E3L067138
Internal ID: LIG001708
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG001708/LIG001708.sdf
Basic Properties
Compound ID
E3L067138
Internal ID
LIG001708
Molecular formula
C13H12N2O3
Molecular weight
244.250000
Exact mass
244.084792
XLogP
0.4476
TPSA
66.4800
HBA / HBD
3 / 1
Rotatable bonds
1
Heavy atoms / rings
18 / 3
Activity summary
IC50 unknown 550.00000000 nM
3 activity record(s) imported
InChIKey
WENKGSGGXGQHSH-UHFFFAOYSA-N
SMILES
O=C1CCC(N2Cc3ccccc3C2=O)C(=O)N1
Aliases
H_EM12 (preferred) BDBM50614095 (source_id) e3_ligand:139 (source_id) MolGlueDB:289 (source_id)
E3 Relation
E3 UniProt Gene / protein Relation type Ligand role Direct Functional Docking Source Evidence
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50614095 medium
; target=Protein cereblon
Q96SW2 CRBN;AD-006
Protein cereblon		 direct_binder e3_ligand Yes Yes medium e3_ligand:139 high
; deduplicated e3_ligand:139 into MolGlueDB:289; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB289 Open -
e3_ligand 139 Open -
BindingDB BDBM50614095 Open - 10.7270/Q2V12923; 10.1021/acsmedchemlett.3c00371; 10.1039/d3md00652b PMID: 36970148; 37974938; 38389883
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM50614095 BDBM50614095 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:139 - exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:289; exact_duplicate; Tanimoto 1.0
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CCC(N2Cc3ccccc3C2=O)C(=O)N1 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG001708/LIG001708.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG001708/LIG001708.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG001708/LIG001708.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG001708/LIG001708.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG001708/LIG001708.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM50614095 IC50 605 nM Moderate DOI: 10.1021/acsmedchemlett.3c00371
PMID: 37974938 		1
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM50614095 IC50 550 nM Moderate DOI: 10.1039/d3md00652b
PMID: 38389883 		1
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM50614095 IC50 605 nM Moderate DOI: 10.7270/Q2V12923
PMID: 36970148 		1