7LWE | pdb_00007lwe

Crystal structure of the BCL6 BTB domain in complex with OICR-7629

• PDB DOI: https://doi.org/10.2210/pdb7LWE/pdb

• Classification: TRANSCRIPTION/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2021-03-01 Released: 2022-03-09 
• Deposition Author(s): Kuntz, D.A., Prive, G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 
  0.131 (Depositor), 0.133 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.117 (DCC) 
• R-Value Observed: 
  0.116 (Depositor) 

Starting Model: experimental

Literature

Discovery of OICR12694: A Novel, Potent, Selective, and Orally Bioavailable BCL6 BTB Inhibitor.

Mamai, A., Chau, A.M., Wilson, B.J., Watson, I.D., Joseph, B.B., Subramanian, P.R., Morshed, M.M., Morin, J.A., Prakesch, M.A., Lu, T., Connolly, P., Kuntz, D.A., Pomroy, N.C., Poda, G., Nguyen, K., Marcellus, R., Strathdee, G., Theriault, B., Subramaniam, R., Mohammed, M., Abibi, A., Chan, M., Winston, J., Kiyota, T., Undzys, E., Aman, A., Austin, N., Du Jardin, M., Packman, K., Phillippar, U., Attar, R., Edwards, J., O'Meara, J., Uehling, D.E., Al-Awar, R., Prive, G.G., Isaac, M.B.

(2023) ACS Med Chem Lett 14: 199-210

• PubMed: 36793435 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00502
• Primary Citation Related Structures: 
  7LWE, 7LWF, 7LWG, 7LZQ, 7LZS


• PubMed Abstract: 
  

  B cell lymphoma 6 (BCL6), a highly regulated transcriptional repressor, is deregulated in several forms of non-Hodgkin lymphoma (NHL), most notably in diffuse large B-cell lymphoma (DLBCL). The activities of BCL6 are dependent on protein-protein interactions with transcriptional co-repressors. To find new therapeutic interventions addressing the needs of patients with DLBCL, we initiated a program to identify BCL6 inhibitors that interfere with co-repressor binding. A virtual screen hit with binding activity in the high micromolar range was optimized by structure-guided methods, resulting in a novel and highly potent inhibitor series. Further optimization resulted in the lead candidate 58 (OICR12694/JNJ-65234637), a BCL6 inhibitor with low nanomolar DLBCL cell growth inhibition and an excellent oral pharmacokinetic profile. Based on its overall favorable preclinical profile, OICR12694 is a highly potent, orally bioavailable candidate for testing BCL6 inhibition in DLBCL and other neoplasms, particularly in combination with other therapies.

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Organizational Affiliation: 
• Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, OntarioM5G 0A3, Canada.
Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania19477, United States.
Princess Margaret Cancer Centre, Toronto, OntarioM5G 2C1, Canada.
Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, OntarioM5S 3M2, Canada.
Janssen Research & Development, Turnhoutseweg 30, B-2340Beerse, Belgium.
Department of Chemistry, University of Toronto, Toronto, OntarioM5S 3H6, Canada.
Department of Pharmacology and Toxicology, University of Toronto, Toronto, OntarioM5S 1A8, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, OntarioM5G 1L7, Canada.
Department of Biochemistry, University of Toronto, Toronto, OntarioM5S 1A8, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 15.32 kDa 
• Atom Count: 1,257 
• Modeled Residue Count: 127 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A	129	Homo sapiens	Mutation(s): 3  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YND (Subject of Investigation/LOI)	B [auth A]	N-(3-chloropyridin-4-yl)-2-(3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)acetamide C14 H12 Cl N5 O2 KGIZMIOMJSGVEF-UHFFFAOYSA-N
ACT	D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
YND	BindingDB:  7LWE	Kd: min: 2.00e+4, max: 2.10e+4 (nM) from 2 assay(s)
		IC50: 2.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free:  0.131 (Depositor), 0.133 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.117 (DCC) 
• R-Value Observed: 0.116 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.606	α = 90
b = 72.113	β = 104.875
c = 55.044	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-09 
Deposition Author(s): Kuntz, D.A., Prive, G.G.

Revision History  

• Version 1.0: 2022-03-09
  Type: Initial release
  
• Version 1.1: 2023-01-25
  Changes: Database references
• Version 1.2: 2023-03-01
  Changes: Database references
• Version 1.3: 2023-10-25
  Changes: Data collection, Refinement description