5X4N | pdb_00005x4n

Crystal structure of the BCL6 BTB domain in complex with Compound 4

• PDB DOI: https://doi.org/10.2210/pdb5X4N/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.209 (Depositor) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.189 (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 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.

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Organizational Affiliation: 
• Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
Takeda California Inc. , 10410 Science Center Dr., San Diego, California 92121, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.57 kDa 
• Atom Count: 1,101 
• Modeled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7ZL	B [auth A]	5-chloro-N4-phenylpyrimidine-2,4-diamine C10 H9 Cl N4 FRISIUXBSNAYFR-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7ZL	BindingDB:  5X4N	Kd: 6.80e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.209 (Depositor) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.602	α = 90
b = 66.602	β = 90
c = 154.609	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, Derived calculations, Refinement description