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13

E3L066559
Internal ID: LIG001129
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG001129/LIG001129.sdf
Basic Properties
Compound ID
E3L066559
Internal ID
LIG001129
Molecular formula
C11H11NO3
Molecular weight
205.213000
Exact mass
205.073893
XLogP
0.8706
TPSA
55.4000
HBA / HBD
3 / 1
Rotatable bonds
2
Heavy atoms / rings
15 / 2
Activity summary
Kd unknown 30000.00000000 nM
5 activity record(s) imported
InChIKey
OXYRJECCEIXMTM-UHFFFAOYSA-N
SMILES
O=C1CCC(Oc2ccccc2)C(=O)N1
Aliases
13 (preferred) BDBM575330 (source_id) e3_ligand:131 (source_id) MolGlueDB:896 (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:BDBM575330 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM575330 medium
; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 direct_binder e3_ligand Yes Yes medium e3_ligand:131 high
; deduplicated e3_ligand:131 into MolGlueDB:896; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB896 Open -
e3_ligand 131 Open - 10.1021/acs.jmedchem.3c01848
BindingDB BDBM575330 Open - 10.7270/Q2H1357Z; 10.7270/Q20869F6; 10.7270/Q24B3549
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM575330 BDBM575330 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:131 - exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:896; exact_duplicate; Tanimoto 1.0
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CCC(Oc2ccccc2)C(=O)N1 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG001129/LIG001129.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG001129/LIG001129.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG001129/LIG001129.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG001129/LIG001129.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG001129/LIG001129.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM575330 Kd 30000 nM Low DOI: 10.7270/Q20869F6 2 source records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM575330 Kd 30000 nM Low DOI: 10.7270/Q2H1357Z 2 source records
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM575330 IC50 55000 nM Low DOI: 10.7270/Q24B3549 1