5N21

Crystal structure of the BCL6 BTB domain in complex with pyrazolo-pyrimidine ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors.

McCoull, W.Abrams, R.D.Anderson, E.Blades, K.Barton, P.Box, M.Burgess, J.Byth, K.Cao, Q.Chuaqui, C.Carbajo, R.J.Cheung, T.Code, E.Ferguson, A.D.Fillery, S.Fuller, N.O.Gangl, E.Gao, N.Grist, M.Hargreaves, D.Howard, M.R.Hu, J.Kemmitt, P.D.Nelson, J.E.O'Connell, N.Prince, D.B.Raubo, P.Rawlins, P.B.Robb, G.R.Shi, J.Waring, M.J.Whittaker, D.Wylot, M.Zhu, X.

(2017) J. Med. Chem. 60: 4386-4402

  • DOI: 10.1021/acs.jmedchem.7b00359
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of the protein-protein interaction between B-cell lymphoma 6 (BCL6) and corepressors has been implicated as a therapeutic target in diffuse large B-cell lymphoma (DLBCL) cancers and profiling of potent and selective BCL6 inhibitors are cri ...

    Inhibition of the protein-protein interaction between B-cell lymphoma 6 (BCL6) and corepressors has been implicated as a therapeutic target in diffuse large B-cell lymphoma (DLBCL) cancers and profiling of potent and selective BCL6 inhibitors are critical to test this hypothesis. We identified a pyrazolo[1,5-a]pyrimidine series of BCL6 binders from a fragment screen in parallel with a virtual screen. Using structure-based drug design, binding affinity was increased 100000-fold. This involved displacing crystallographic water, forming new ligand-protein interactions and a macrocyclization to favor the bioactive conformation of the ligands. Optimization for slow off-rate constant kinetics was conducted as well as improving selectivity against an off-target kinase, CK2. Potency in a cellular BCL6 assay was further optimized to afford highly selective probe molecules. Only weak antiproliferative effects were observed across a number of DLBCL lines and a multiple myeloma cell line without a clear relationship to BCL6 potency. As a result, we conclude that the BCL6 hypothesis in DLBCL cancer remains unproven.


    Organizational Affiliation

    IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K.,IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K.,IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States.,Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China.




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
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
8HN
Query on 8HN

Download SDF File 
Download CCD File 
A, B
2-[(2~{S})-1-[3-cyano-7-[(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)amino]pyrazolo[1,5-a]pyrimidin-5-yl]pyrrolidin-2-yl]ethanoic acid
C22 H21 N7 O3
HZSGYGFOUDGOKL-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8HNIC50: 350 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 30.400α = 83.36
b = 38.970β = 75.39
c = 54.930γ = 67.21
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Data collection, Database references