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dBET-1

E3L066297
Internal ID: LIG000867
MGD Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG000867/LIG000867.sdf
Basic Properties
Compound ID
E3L066297
Internal ID
LIG000867
Molecular formula
C38H37ClN8O7S
Molecular weight
785.283000
Exact mass
784.219444
XLogP
3.6825
TPSA
194.0500
HBA / HBD
11 / 3
Rotatable bonds
12
Heavy atoms / rings
55 / 7
Activity summary
IC50 unknown 3.09000000 nM
4 activity record(s) imported
InChIKey
LKEGXJXRNBALBV-PMCHYTPCSA-N
SMILES
Cc1sc2c(c1C)C(c1ccc(Cl)cc1)=N[C@@H](CC(=O)NCCCCNC(=O)COc1cccc3c1C(=O)N(C1CCC(=O)NC1=O)C3=O)c1nnc(C)n1-2
Aliases
dBET-1 (preferred) 4a(dBET1) (synonym) 4a(dBET1) (source_name) BDBM50544938 (source_id) MolGlueDB:263 (source_id) MolGlueDB:263 (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:BDBM50544938 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50544938 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB263 Open -
BindingDB BDBM50544938 Open - 10.7270/Q2G44TFM
BindingDB
Related evidence		 BDBM511595 Open - 10.7270/Q2G44TFM
high_similarity_chiral_candidate; Tanimoto 0.956522
BindingDB
Related evidence		 BDBM511596 Open - 10.7270/Q2G44TFM
same_connectivity_stereo_or_protonation_diff; Tanimoto 1.000000
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM50544938 BDBM50544938 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:BDBM511596 BDBM511596 same_connectivity_stereo_or_protonation_diff keep_bindingdb_stereo_or_protonation_variant - Connectivity InChIKey matches, but full InChIKey/isomeric SMILES differs
BindingDB:BDBM511596 BDBM511596 same_connectivity_stereo_or_protonation_diff keep_bindingdb_stereo_or_protonation_variant 1.000000
chiral 0.895833 		Morgan non-chiral Tanimoto >= 0.95; retained for SAR/stereo review
BindingDB:BDBM511595 BDBM511595 high_similarity_chiral_candidate keep_bindingdb_high_similarity_candidate 0.956522
chiral 0.956522 		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 Cc1sc2c(c1C)C(c1ccc(Cl)cc1)=N[C@@H](CC(=O)NCCCCNC(=O)COc1cccc3c1C(=O)N(C1CCC(=O)NC1=O)C3=O)c1nnc(C)n1-2 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG000867/LIG000867.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG000867/LIG000867.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG000867/LIG000867.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG000867/LIG000867.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG000867/LIG000867.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM50544938 IC50 20 nM High DOI: 10.7270/Q2G44TFM 2 source records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM50544938 IC50 3.09 nM Very high DOI: 10.7270/Q2G44TFM 2 source records