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22

E3L066165
Internal ID: LIG000735
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG000735/LIG000735.sdf
Basic Properties
Compound ID
E3L066165
Internal ID
LIG000735
Molecular formula
C13H13N3O2
Molecular weight
243.266000
Exact mass
243.100777
XLogP
1.0935
TPSA
63.9900
HBA / HBD
3 / 1
Rotatable bonds
1
Heavy atoms / rings
18 / 3
Activity summary
Kd < 10000.00000000 nM
2 activity record(s) imported
InChIKey
JPHZXDBBLIMTNU-UHFFFAOYSA-N
SMILES
Cn1nc(C2CCC(=O)NC2=O)c2ccccc21
Aliases
22 (preferred) BDBM475126 (source_id) e3_ligand:150 (source_id) MolGlueDB:590 (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:BDBM475126 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM475126 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 direct_binder e3_ligand Yes Yes medium e3_ligand:150 high
; deduplicated e3_ligand:150 into MolGlueDB:590; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB590 Open -
e3_ligand 150 Open - 10.1021/acs.jmedchem.3c01848
BindingDB BDBM475126 Open - 10.7270/Q2P84FZ1
BindingDB
Related evidence		 BDBM475127 Open - 10.7270/Q2P84FZ1
same_connectivity_stereo_or_protonation_diff; Tanimoto 1.000000
BindingDB
Related evidence		 BDBM475128 Open - 10.7270/Q2P84FZ1
same_connectivity_stereo_or_protonation_diff; Tanimoto 1.000000
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM475126 BDBM475126 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:150 - exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:590; exact_duplicate; Tanimoto 1.0
BindingDB:BDBM475127 BDBM475127 same_connectivity_stereo_or_protonation_diff keep_bindingdb_stereo_or_protonation_variant - Connectivity InChIKey matches, but full InChIKey/isomeric SMILES differs
BindingDB:BDBM475127 BDBM475127 same_connectivity_stereo_or_protonation_diff keep_bindingdb_stereo_or_protonation_variant 1.000000
chiral 0.948718 		Morgan non-chiral Tanimoto >= 0.95; retained for SAR/stereo review
BindingDB:BDBM475128 BDBM475128 same_connectivity_stereo_or_protonation_diff keep_bindingdb_stereo_or_protonation_variant - Connectivity InChIKey matches, but full InChIKey/isomeric SMILES differs
BindingDB:BDBM475128 BDBM475128 same_connectivity_stereo_or_protonation_diff keep_bindingdb_stereo_or_protonation_variant 1.000000
chiral 0.948718 		Morgan non-chiral Tanimoto >= 0.95; retained for SAR/stereo review
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready Cn1nc(C2CCC(=O)NC2=O)c2ccccc21 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG000735/LIG000735.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG000735/LIG000735.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG000735/LIG000735.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG000735/LIG000735.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG000735/LIG000735.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM475126 Kd <10000 nM Uncertain DOI: 10.7270/Q2P84FZ1 2 source records