5X4P

Crystal structure of the BCL6 BTB domain in complex with Compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach

Kamada, Y.Sakai, N.Sogabe, S.Ida, K.Oki, H.Sakamoto, K.Lane, W.Snell, G.Iida, M.Imaeda, Y.Sakamoto, J.Matsui, J.

(2017) J Med Chem 60: 4358-4368

  • DOI: 10.1021/acs.jmedchem.7b00313
  • Primary Citation of Related Structures:  
    5X4M, 5X4N, 5X4O, 5X4P, 5X4Q

  • PubMed Abstract: 
  • B-cell lymphoma 6 (BCL6) is a transcriptional factor that expresses in lymphocytes and regulates the differentiation and proliferation of lymphocytes. Therefore, BCL6 is a therapeutic target for autoimmune diseases and cancer treatment. This report presents the discovery of BCL6-corepressor interaction inhibitors by using a biophysics-driven fragment-based approach ...

    B-cell lymphoma 6 (BCL6) is a transcriptional factor that expresses in lymphocytes and regulates the differentiation and proliferation of lymphocytes. Therefore, BCL6 is a therapeutic target for autoimmune diseases and cancer treatment. This report presents the discovery of BCL6-corepressor interaction inhibitors by using a biophysics-driven fragment-based approach. Using the surface plasmon resonance (SPR)-based fragment screening, we successfully identified fragment 1 (SPR K D = 1200 μM, ligand efficiency (LE) = 0.28), a competitive binder to the natural ligand BCoR peptide. Moreover, we elaborated 1 into the more potent compound 7 (SPR K D = 0.078 μM, LE = 0.37, cell-free protein-protein interaction (PPI) IC 50 = 0.48 μM (ELISA), cellular PPI IC 50 = 8.6 μM (M2H)) by a structure-based design and structural integration with a second high-throughput screening hit.


    Organizational Affiliation

    Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B-cell lymphoma 6 proteinA141Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7ZO (Subject of Investigation/LOI)
Query on 7ZO

Download Ideal Coordinates CCD File 
B [auth A]5-[(5-chloranylpyrimidin-4-yl)amino]-1,3-dihydroindol-2-one
C12 H9 Cl N4 O
XGLOINXVRYWOSM-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
7ZO BindingDB:  5X4P Kd: 9300 (nM) from 1 assay(s)
Binding MOAD:  5X4P Kd: 9300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.728α = 90
b = 66.728β = 90
c = 155.325γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references