6EW7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/acschembio.8b00698
  • Primary Citation of Related Structures:  

  • 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 targ ...

    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.,Pelago Bioscience AB , Banvaktsvägen 20 , 17148 Solna , Sweden.,Oncology and Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gatehouse Park , Waltham , Massachusetts 02451 , United States.,Oncology and Discovery Sciences, IMED Biotech Unit , AstraZeneca , 310 Cambridge Science Park, Milton Road , Cambridge CB4 0WG , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B-cell lymphoma 6 protein
A, B
122Homo sapiensMutation(s): 0 
Gene Names: BCL6 (BCL5, LAZ3, ZBTB27, ZNF51)
Find proteins for P41182 (Homo sapiens)
Go to Gene View: BCL6
Go to UniProtKB:  P41182
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C1W
Query on C1W

Download SDF File 
Download CCD File 
A, B
2-chloranyl-4-[[5-chloranyl-4-[(4-fluorophenyl)amino]pyrimidin-2-yl]amino]benzoic acid
C17 H11 Cl2 F N4 O2
WDFNHFCRBOZIRF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 30.780α = 83.98
b = 39.290β = 73.95
c = 55.430γ = 67.11
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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