5X9O | pdb_00005x9o

Crystal structure of the BCL6 BTB domain in complex with Compound 1a

• PDB DOI: https://doi.org/10.2210/pdb5X9O/pdb

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


• Deposited: 2017-03-08 Released: 2017-08-16 
• Deposition Author(s): Sogabe, S., Ida, K., Lane, W., Snell, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.213 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design

Yasui, T., Yamamoto, T., Sakai, N., Asano, K., Takai, T., Yoshitomi, Y., Davis, M., Takagi, T., Sakamoto, K., Sogabe, S., Kamada, Y., Lane, W., Snell, G., Iwata, M., Goto, M., Inooka, H., Sakamoto, J.I., Nakada, Y., Imaeda, Y.

(2017) Bioorg Med Chem 25: 4876-4886

• PubMed: 28760529 
• DOI: https://doi.org/10.1016/j.bmc.2017.07.037
• Primary Citation Related Structures: 
  5X9O, 5X9P


• PubMed Abstract: 
  

  B-cell lymphoma 6 (BCL6) is a transcriptional repressor that can form complexes with corepressors via protein-protein interactions (PPIs). The complexes of BCL6 and corepressors play an important role in the formation of germinal centers (GCs), and differentiation and proliferation of lymphocytes. Therefore, BCL6-corepressor interaction inhibitors would be drug candidates for managing autoimmune diseases and cancer. Starting from high-throughput screening hits 1a and 2a, we identified a novel BCL6-corepressor interaction inhibitor 8c (cell-free enzyme-linked immunosorbent assay [ELISA] IC ₅₀ =0.10µM, cell-based mammalian two-hybrid [M2H] assay IC ₅₀ =0.72µM) by utilizing structure-based drug design (SBDD) based on an X-ray crystal structure of 1a bound to BCL6. Compound 8c also showed a good pharmacokinetic profile, which was acceptable for both in vitro and in vivo studies.

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Organizational Affiliation: 
• Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: [e-mail].
Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
Takeda California Inc., 10410 Science Center Dr., San Diego, CA 92121, USA.
Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.69 kDa 
• Atom Count: 1,196 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
80R	B [auth A]	5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one C13 H9 Cl N4 O3 LBXJVISQYZQJLT-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
80R	BindingDB:  5X9O	Kd: 5000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.213 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.618	α = 90
b = 66.618	β = 90
c = 151.996	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: 2017-08-16 
Deposition Author(s): Sogabe, S., Ida, K., Lane, W., Snell, G.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description