Crystal structure of the BCL6 BTB domain in complex with anilinopyrimidine ligand

Experimental Data Snapshot

  • Resolution: 1.39 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Development of a Novel B-Cell Lymphoma 6 (BCL6) PROTAC To Provide Insight into Small Molecule Targeting of BCL6.

McCoull, W.Cheung, T.Anderson, E.Barton, P.Burgess, J.Byth, K.Cao, Q.Castaldi, M.P.Chen, H.Chiarparin, E.Carbajo, R.J.Code, E.Cowan, S.Davey, P.R.Ferguson, A.D.Fillery, S.Fuller, N.O.Gao, N.Hargreaves, D.Howard, M.R.Hu, J.Kawatkar, A.Kemmitt, P.D.Leo, E.Molina, D.M.O'Connell, N.Petteruti, P.Rasmusson, T.Raubo, P.Rawlins, P.B.Ricchiuto, P.Robb, G.R.Schenone, M.Waring, M.J.Zinda, M.Fawell, S.Wilson, D.M.

(2018) ACS Chem Biol 13: 3131-3141

  • DOI: https://doi.org/10.1021/acschembio.8b00698
  • Primary Citation of Related Structures:  
    6EW6, 6EW7, 6EW8

  • PubMed Abstract: 

    B-cell lymphoma 6 (BCL6) inhibition is a promising mechanism for treating hematological cancers but high quality chemical probes are necessary to evaluate its therapeutic potential. Here we report potent BCL6 inhibitors that demonstrate cellular target engagement and exhibit exquisite selectivity for BCL6 based on mass spectrometry analyses following chemical proteomic pull down. Importantly, a proteolysis-targeting chimera (PROTAC) was also developed and shown to significantly degrade BCL6 in a number of diffuse large B-cell lymphoma (DLBCL) cell lines, but neither BCL6 inhibition nor degradation selectively induced marked phenotypic response. To investigate, we monitored PROTAC directed BCL6 degradation in DLBCL OCI-Ly1 cells by immunofluorescence and discovered a residual BCL6 population. Analysis of subcellular fractions also showed incomplete BCL6 degradation in all fractions despite having measurable PROTAC concentrations, together providing a rationale for the weak antiproliferative response seen with both BCL6 inhibitor and degrader. In summary, we have developed potent and selective BCL6 inhibitors and a BCL6 PROTAC that effectively degraded BCL6, but both modalities failed to induce a significant phenotypic response in DLBCL despite achieving cellular concentrations.

  • Organizational Affiliation

    Broad Institute of Harvard and MIT , 7 Cambridge Center , Cambridge , Massachusetts 02142 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein123Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens)
Explore P41182 
Go to UniProtKB:  P41182
PHAROS:  P41182
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41182
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C0H

Download Ideal Coordinates CCD File 
B [auth A]~{N}2-(2-chlorophenyl)-1,3,5-triazine-2,4-diamine
C9 H8 Cl N5
Binding Affinity Annotations 
IDSourceBinding Affinity
C0H Binding MOAD:  6EW6 Kd: 8.29e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.39 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.54α = 90
b = 73.01β = 104.23
c = 53.54γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references