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compound 10

E3L067054
Internal ID: LIG001624
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG001624/LIG001624.sdf
Basic Properties
Compound ID
E3L067054
Internal ID
LIG001624
Molecular formula
C13H13N3O3
Molecular weight
259.265000
Exact mass
259.095691
XLogP
0.3177
TPSA
73.1000
HBA / HBD
3 / 1
Rotatable bonds
1
Heavy atoms / rings
19 / 3
Activity summary
IC50 < 1000.00000000 nM
9 activity record(s) imported
InChIKey
VFDZUWPTOYTMAL-UHFFFAOYSA-N
SMILES
Cn1c(=O)n(C2CCC(=O)NC2=O)c2ccccc21
Aliases
compound 10 (preferred) BDBM557564 (source_id) e3_ligand:89 (source_id) MolGlueDB:545 (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:BDBM557564 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM557564 medium
; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 direct_binder e3_ligand Yes Yes medium e3_ligand:89 high
; deduplicated e3_ligand:89 into MolGlueDB:545; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB545 Open -
e3_ligand 89 Open -
BindingDB BDBM557564 Open - 10.7270/Q23T9MFH; 10.7270/Q2HT2T8T; 10.7270/Q2FN1BRK
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM557564 BDBM557564 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:89 - exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:545; exact_duplicate; Tanimoto 1.0
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready Cn1c(=O)n(C2CCC(=O)NC2=O)c2ccccc21 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG001624/LIG001624.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG001624/LIG001624.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG001624/LIG001624.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG001624/LIG001624.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG001624/LIG001624.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM557564 IC50 <1000 nM Uncertain DOI: 10.7270/Q2HT2T8T 2 source records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM557564 IC50 <1000 nM Uncertain DOI: 10.7270/Q23T9MFH 4 source records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM557564 Kd <10000 nM Uncertain DOI: 10.7270/Q2FN1BRK 2 source records
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM557564 IC50 <1000 nM Uncertain DOI: 10.7270/Q2HT2T8T 1