5X4O

Crystal structure of the BCL6 BTB domain in complex with Compound 5

• PDB DOI: https://doi.org/10.2210/pdb5X4O/pdb

• Classification: Transcription/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-13 Released: 2017-05-24 
• Deposition Author(s): Sogabe, S., Ida, K., Lane, W., Snell, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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

• PubMed: 28471657 
• DOI: https://doi.org/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. 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.8 kDa 
• Atom Count: 1,108 
• Modelled Residue Count: 130 
• Deposited Residue Count: 141 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A	141	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 GTEx:  ENSG00000113916

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YAM	B [auth A]	N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide C21 H20 F3 N7 O3 S MZDKLVOWGIOKTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YAM	BindingDB:  5X4O	Kd: 8.80e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.439	α = 90
b = 66.439	β = 90
c = 152.797	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Sogabe, S., Ida, K., Lane, W., Snell, G.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description