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5

E3L066854
Internal ID: LIG001424
MGD Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG001424/LIG001424.sdf
Basic Properties
Compound ID
E3L066854
Internal ID
LIG001424
Molecular formula
C25H25N5O3
Molecular weight
443.507000
Exact mass
443.195740
XLogP
2.5867
TPSA
98.4000
HBA / HBD
5 / 2
Rotatable bonds
4
Heavy atoms / rings
33 / 6
Activity summary
IC50 unknown 20.00000000 nM
2 activity record(s) imported
InChIKey
SNZGVVSAMPFNLQ-UHFFFAOYSA-N
SMILES
O=C1CCC(N2Cc3cc(-c4cc(CN5CCCC5)c5cc[nH]c5n4)ccc3C2=O)C(=O)N1
Aliases
5 (preferred) BDBM755856 (source_id) MolGlueDB:1496 (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:BDBM755856 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM755856 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB1496 Open -
BindingDB BDBM755856 Open - 10.7270/Q2WM1K1R
BindingDB
Related evidence		 BDBM755905 Open - 10.7270/Q2WM1K1R
high_similarity_chiral_candidate; Tanimoto 0.968254
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM755856 BDBM755856 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
BindingDB:BDBM755905 BDBM755905 high_similarity_chiral_candidate keep_bindingdb_high_similarity_candidate 0.968254
chiral 0.968254 		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 O=C1CCC(N2Cc3cc(-c4cc(CN5CCCC5)c5cc[nH]c5n4)ccc3C2=O)C(=O)N1 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG001424/LIG001424.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG001424/LIG001424.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG001424/LIG001424.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG001424/LIG001424.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG001424/LIG001424.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM755856 IC50 20 nM High DOI: 10.7270/Q2WM1K1R 2 source records