7BDE

HUMAN BCL6 BTB-DOMAIN IN COMPLEX WITH GSK137


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

GSK137, a potent small-molecule BCL6 inhibitor with in vivo activity, suppresses antibody responses in mice.

Pearce, A.C.Bamford, M.J.Barber, R.Bridges, A.Convery, M.A.Demetriou, C.Evans, S.Gobbetti, T.Hirst, D.J.Holmes, D.S.Hutchinson, J.P.Jayne, S.Lezina, L.McCabe, M.T.Messenger, C.Morley, J.Musso, M.C.Scott-Stevens, P.Manso, A.S.Schofield, J.Slocombe, T.Somers, D.Walker, A.L.Wyce, A.Zhang, X.P.Wagner, S.D.

(2021) J Biol Chem 297: 100928-100928

  • DOI: https://doi.org/10.1016/j.jbc.2021.100928
  • Primary Citation of Related Structures:  
    7BDE

  • PubMed Abstract: 

    B-cell lymphoma 6 (BCL6) is a zinc finger transcriptional repressor possessing a BTB-POZ (BR-C, ttk, and bab for BTB; pox virus and zinc finger for POZ) domain, which is required for homodimerization and association with corepressors. BCL6 has multiple roles in normal immunity, autoimmunity, and some types of lymphoma. Mice bearing disrupted BCL6 loci demonstrate suppressed high-affinity antibody responses to T-dependent antigens. The corepressor binding groove in the BTB-POZ domain is a potential target for small compound-mediated therapy. Several inhibitors targeting this binding groove have been described, but these compounds have limited or absent in vivo activity. Biophysical studies of a novel compound, GSK137, showed an in vitro pIC 50 of 8 and a cellular pIC 50 of 7.3 for blocking binding of a peptide derived from the corepressor silencing mediator for retinoid or thyroid hormone receptors to the BCL6 BTB-POZ domain. The compound has good solubility (128 μg/ml) and permeability (86 nM/s). GSK137 caused little change in cell viability or proliferation in four BCL6-expressing B-cell lymphoma lines, although there was modest dose-dependent accumulation of G1 phase cells. Pharmacokinetic studies in mice showed a profile compatible with achieving good levels of target engagement. GSK137, administered orally, suppressed immunoglobulin G responses and reduced numbers of germinal centers and germinal center B cells following immunization of mice with the hapten trinitrophenol. Overall, we report a novel small-molecule BCL6 inhibitor with in vivo activity that inhibits the T-dependent antigen immune response.


  • Organizational Affiliation

    GlaxoSmithKline, Medicines Research Centre, Stevenage, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of B-cell lymphoma 6 protein135Homo 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
TEQ (Subject of Investigation/LOI)
Query on TEQ

Download Ideal Coordinates CCD File 
B [auth A]5-[(5S,7R)-3-fluoranyl-7-(2-methylpyridin-3-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidin-5-yl]quinolin-2-amine
C21 H19 F N6
WSRZNMRSHUJOED-RBUKOAKNSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TEQ BindingDB:  7BDE IC50: min: 10, max: 25 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.251α = 90
b = 49.251β = 90
c = 124.409γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata processing
Aimlessdata reduction
STARANISOdata scaling
REFMACrefinement
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-07-28 
  • Deposition Author(s): Somers, D.O.

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description