5MWD

Crystal structure of the BCL6 BTB-domain with compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1016/j.celrep.2017.08.081
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B-cell lymphoma 6 protein
A
126Homo sapiensMutation(s): 3 
Gene Names: BCL6 (BCL5, LAZ3, ZBTB27, ZNF51)
Find proteins for P41182 (Homo sapiens)
Go to Gene View: BCL6
Go to UniProtKB:  P41182
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TJ3
Query on TJ3

Download SDF File 
Download CCD File 
A
5-[[5-chloranyl-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-yl]amino]-1,3-dihydroindol-2-one
C17 H15 Cl N6 O
UHUDVGHKSUEYOT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 30.311α = 90.00
b = 71.761β = 105.95
c = 54.873γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release