Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 14.82 kDa 
• Atom Count: 1135 
• Modelled Residue Count: 123 
• Deposited Residue Count: 124 
• Unique protein chains: 1

6EW8

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

• PDB DOI: 10.2210/pdb6EW8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-03 Released: 2018-10-24 
• Deposition Author(s): Robb, G., Ferguson, A., Hargreaves, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.244 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

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

• PubMed: 30335946 
• DOI: 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.

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Organizational Affiliation: 

Oncology and Discovery Sciences, IMED Biotech Unit , AstraZeneca , 310 Cambridge Science Park, Milton Road , Cambridge CB4 0WG , U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A	124	Homo sapiens	Mutation(s): 0  Gene Names: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens) Explore P41182  Go to UniProtKB:  P41182
PHAROS:  P41182

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C0Q	C [auth A]	anilinopyrimidine ligand C21 H25 Cl N6 O3 HEBYPYJZLRAGKE-OAHLLOKOSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.244 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.668	α = 90
b = 73.017	β = 104.55
c = 53.995	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-11-03 
• Released Date: 2018-10-24 
Deposition Author(s): Robb, G., Ferguson, A., Hargreaves, D.

Revision History  

• 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