7LZS

Crystal structure of the BCL6 BTB domain in complex with OICR-11029


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

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

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00502
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein125Homo sapiensMutation(s): 3 
Gene Names: BCL6BCL5LAZ3ZBTB27ZNF51
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41182
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YJS (Subject of Investigation/LOI)
Query on YJS

Download Ideal Coordinates CCD File 
B [auth A]3-chloro-5-{7-[2-({5-chloro-2-[(3S)-3-methylmorpholin-4-yl]pyridin-4-yl}amino)-2-oxoethyl]-3-methyl-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-hydroxybenzamide
C26 H25 Cl2 N7 O5
NDRFFOKFYGUOKD-ZDUSSCGKSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.907α = 90
b = 72.425β = 104.588
c = 54.816γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    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