7ZWW

Crystal structure of human BCL6 BTB domain in complex with compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays.

Pierrat, O.A.Liu, M.Collie, G.W.Shetty, K.Rodrigues, M.J.Le Bihan, Y.V.Gunnell, E.A.McAndrew, P.C.Stubbs, M.Rowlands, M.G.Yahya, N.Shehu, E.Talbot, R.Pickard, L.Bellenie, B.R.Cheung, K.J.Drouin, L.Innocenti, P.Woodward, H.Davis, O.A.Lloyd, M.G.Varela, A.Huckvale, R.Broccatelli, F.Carter, M.Galiwango, D.Hayes, A.Raynaud, F.I.Bryant, C.Whittaker, S.Rossanese, O.W.Hoelder, S.Burke, R.van Montfort, R.L.M.

(2022) Sci Rep 12: 18633-18633

  • DOI: https://doi.org/10.1038/s41598-022-23264-z
  • Primary Citation of Related Structures:  
    7ZWN, 7ZWO, 7ZWP, 7ZWQ, 7ZWR, 7ZWS, 7ZWT, 7ZWU, 7ZWV, 7ZWW, 7ZWX, 7ZWY, 7ZWZ

  • PubMed Abstract: 

    By suppressing gene transcription through the recruitment of corepressor proteins, B-cell lymphoma 6 (BCL6) protein controls a transcriptional network required for the formation and maintenance of B-cell germinal centres. As BCL6 deregulation is implicated in the development of Diffuse Large B-Cell Lymphoma, we sought to discover novel small molecule inhibitors that disrupt the BCL6-corepressor protein-protein interaction (PPI). Here we report our hit finding and compound optimisation strategies, which provide insight into the multi-faceted orthogonal approaches that are needed to tackle this challenging PPI with small molecule inhibitors. Using a 1536-well plate fluorescence polarisation high throughput screen we identified multiple hit series, which were followed up by hit confirmation using a thermal shift assay, surface plasmon resonance and ligand-observed NMR. We determined X-ray structures of BCL6 bound to compounds from nine different series, enabling a structure-based drug design approach to improve their weak biochemical potency. We developed a time-resolved fluorescence energy transfer biochemical assay and a nano bioluminescence resonance energy transfer cellular assay to monitor cellular activity during compound optimisation. This workflow led to the discovery of novel inhibitors with respective biochemical and cellular potencies (IC 50s ) in the sub-micromolar and low micromolar range.


  • Organizational Affiliation

    Division of Cancer Therapeutics, Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein144Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.6α = 90
b = 67.6β = 90
c = 166.7γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A11566

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description