7LWG | pdb_00007lwg

Crystal structure of the BCL6 BTB domain in complex with OICR-12694

PDB DOI: https://doi.org/10.2210/pdb7LWG/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.184 (Depositor), 0.185 (DCC)
R-Value Work:
0.144 (Depositor), 0.145 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

Drug Discovery Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, OntarioM5G 0A3, Canada.

Macromolecule Content

Total Structure Weight: 30.38 kDa
Atom Count: 2,361
Modeled Residue Count: 243
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A, B	125	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41182
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YN7 (Subject of Investigation/LOI) Query on YN7 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	5-{(5S)-1-[2-({3-chloro-6-[(2S)-2,4-dimethylpiperazin-1-yl]-2-fluoropyridin-4-yl}amino)-2-oxoethyl]-4-oxo-4,6,7,8-tetrahydro-1H-dipyrrolo[1,2-a:2',3'-d]pyrimidin-3-yl}-3,4-difluoro-2-hydroxybenzamide C₂₉ H₂₈ Cl F₃ N₈ O₄ LGAFZGSECXDYIR-ZDUSSCGKSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], J [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]