6CQ1

BCL6 BTB domain in complex with 15a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.

Cheng, H.Linhares, B.M.Yu, W.Cardenas, M.G.Ai, Y.Jiang, W.Winkler, A.Cohen, S.Melnick, A.MacKerell Jr., A.Cierpicki, T.Xue, F.

(2018) J Med Chem 61: 7573-7588

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00040
  • Primary Citation of Related Structures:  
    6C3L, 6C3N, 6CQ1

  • PubMed Abstract: 

    Protein-protein interactions (PPI) between the transcriptional repressor B-cell lymphoma 6 (BCL6) BTB domain (BCL6 BTB ) and its corepressors have emerged as a promising target for anticancer therapeutics. However, identification of potent, drug-like inhibitors of BCL6 BTB has remained challenging. Using NMR-based screening of a library of fragment-like small molecules, we have identified a thiourea compound (7CC5) that binds to BCL6 BTB . From this hit, the application of computer-aided drug design (CADD), medicinal chemistry, NMR spectroscopy, and X-ray crystallography has yielded an inhibitor, 15f, that demonstrated over 100-fold improved potency for BCL6 BTB . This gain in potency was achieved by a unique binding mode that mimics the binding mode of the corepressor SMRT in the aromatic and the HDCH sites. The structure-activity relationship based on these new inhibitors will have a significant impact on the rational design of novel BCL6 inhibitors, facilitating the identification of therapeutics for the treatment of BCL6-dependent tumors.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein
A, B
131Homo sapiensMutation(s): 4 
Gene Names: BCL6BCL5LAZ3ZBTB27ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens)
Explore P41182 
Go to UniProtKB:  P41182
PHAROS:  P41182
GTEx:  ENSG00000113916 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41182
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F8J
Query on F8J

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-{6-({[2-(1H-indol-3-yl)ethyl]carbamothioyl}amino)-3-[(4-methylpiperazin-1-yl)methyl]-1H-indol-1-yl}-N-(propan-2-yl)acetamide
C30 H39 N7 O S
DCSGGGDRUYCRAM-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
F8J Binding MOAD:  6CQ1 Kd: 2.19e+5 (nM) from 1 assay(s)
BindingDB:  6CQ1 Kd: 2.19e+5 (nM) from 1 assay(s)
IC50: 1.42e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.012α = 83.654
b = 39.621β = 73.633
c = 55.225γ = 66.98
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description