Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Chemically Induced Degradation of the Oncogenic Transcription Factor BCL6.

Kerres, N.Steurer, S.Schlager, S.Bader, G.Berger, H.Caligiuri, M.Dank, C.Engen, J.R.Ettmayer, P.Fischerauer, B.Flotzinger, G.Gerlach, D.Gerstberger, T.Gmaschitz, T.Greb, P.Han, B.Heyes, E.Iacob, R.E.Kessler, D.Kolle, H.Lamarre, L.Lancia, D.R.Lucas, S.Mayer, M.Mayr, K.Mischerikow, N.Muck, K.Peinsipp, C.Petermann, O.Reiser, U.Rudolph, D.Rumpel, K.Salomon, C.Scharn, D.Schnitzer, R.Schrenk, A.Schweifer, N.Thompson, D.Traxler, E.Varecka, R.Voss, T.Weiss-Puxbaum, A.Winkler, S.Zheng, X.Zoephel, A.Kraut, N.McConnell, D.Pearson, M.Koegl, M.

(2017) Cell Rep 20: 2860-2875

  • DOI: https://doi.org/10.1016/j.celrep.2017.08.081
  • Primary Citation of Related Structures:  
    5MW2, 5MW6, 5MWD

  • PubMed Abstract: 

    The transcription factor BCL6 is a known driver of oncogenesis in lymphoid malignancies, including diffuse large B cell lymphoma (DLBCL). Disruption of its interaction with transcriptional repressors interferes with the oncogenic effects of BCL6. We used a structure-based drug design to develop highly potent compounds that block this interaction. A subset of these inhibitors also causes rapid ubiquitylation and degradation of BCL6 in cells. These compounds display significantly stronger induction of expression of BCL6-repressed genes and anti-proliferative effects than compounds that merely inhibit co-repressor interactions. This work establishes the BTB domain as a highly druggable structure, paving the way for the use of other members of this protein family as drug targets. The magnitude of effects elicited by this class of BCL6-degrading compounds exceeds that of our equipotent non-degrading inhibitors, suggesting opportunities for the development of BCL6-based lymphoma therapeutics.

  • Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein126Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens)
Explore P41182 
Go to UniProtKB:  P41182
GTEx:  ENSG00000113916 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41182
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on U52

Download Ideal Coordinates CCD File 
B [auth A]2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide
C24 H29 Cl N6 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.367α = 90
b = 72.657β = 105.87
c = 54.883γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Refinement description