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8

E3L066051
Internal ID: LIG000621
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG000621/LIG000621.sdf
Basic Properties
Compound ID
E3L066051
Internal ID
LIG000621
Molecular formula
C13H11N3O4
Molecular weight
273.248000
Exact mass
273.074956
XLogP
-0.3300
TPSA
109.5700
HBA / HBD
5 / 2
Rotatable bonds
1
Heavy atoms / rings
20 / 3
Activity summary
IC50 unknown 95.00000000 nM
5 activity record(s) imported
InChIKey
IICWMVJMJVXCLY-UHFFFAOYSA-N
SMILES
Nc1ccc2c(c1)C(=O)N(C1CCC(=O)NC1=O)C2=O
Aliases
8 (preferred) 5-NH2-Thal (synonym) 5-NH2-Thal (source_name) BDBM511643 (source_id) e3_ligand:58 (source_id) MolGlueDB:809 (source_id) MolGlueDB:809 (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:BDBM511643 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM511643 medium
; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 direct_binder e3_ligand Yes Yes medium e3_ligand:58 high
; deduplicated e3_ligand:58 into MolGlueDB:809; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB809 Open -
e3_ligand 58 Open - 10.1002/cmdc.201800271
BindingDB BDBM511643 Open - 10.7270/Q2G44TFM; 10.7270/Q2FN1BRK; 10.7270/Q2V12923 PMID: 36970148
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM511643 BDBM511643 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:58 - exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:809; exact_duplicate; Tanimoto 1.0
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready Nc1ccc2c(c1)C(=O)N(C1CCC(=O)NC1=O)C2=O keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG000621/LIG000621.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG000621/LIG000621.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG000621/LIG000621.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG000621/LIG000621.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG000621/LIG000621.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM511643 IC50 95 nM High DOI: 10.7270/Q2G44TFM 2 source records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM511643 Kd <10000 nM Uncertain DOI: 10.7270/Q2FN1BRK 2 source records
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM511643 IC50 560 nM Moderate DOI: 10.7270/Q2V12923
PMID: 36970148 		1