3LBZ

Crystal Structure of the BCL6 BTB domain complexed with the small molecule inhibitor 79-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo.

Cerchietti, L.C.Ghetu, A.F.Zhu, X.Da Silva, G.F.Zhong, S.Matthews, M.Bunting, K.L.Polo, J.M.Fares, C.Arrowsmith, C.H.Yang, S.N.Garcia, M.Coop, A.Mackerell, A.D.Prive, G.G.Melnick, A.

(2010) Cancer Cell 17: 400-411

  • DOI: 10.1016/j.ccr.2009.12.050

  • PubMed Abstract: 
  • The BCL6 transcriptional repressor is the most frequently involved oncogene in diffuse large B cell lymphoma (DLBCL). We combined computer-aided drug design with functional assays to identify low-molecular-weight compounds that bind to the corepresso ...

    The BCL6 transcriptional repressor is the most frequently involved oncogene in diffuse large B cell lymphoma (DLBCL). We combined computer-aided drug design with functional assays to identify low-molecular-weight compounds that bind to the corepressor binding groove of the BCL6 BTB domain. One such compound disrupted BCL6/corepressor complexes in vitro and in vivo, and was observed by X-ray crystallography and NMR to bind the critical site within the BTB groove. This compound could induce expression of BCL6 target genes and kill BCL6-positive DLBCL cell lines. In xenotransplantation experiments, the compound was nontoxic and potently suppressed DLBCL tumors in vivo. The compound also killed primary DLBCLs from human patients.


    Organizational Affiliation

    Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B-cell lymphoma 6 protein
A, B
127Homo sapiensGene Names: BCL6 (BCL5, LAZ3, ZBTB27, ZNF51)
Find proteins for P41182 (Homo sapiens)
Go to Gene View: BCL6
Go to UniProtKB:  P41182
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z89
Query on Z89

Download SDF File 
Download CCD File 
A, B
(2R)-2-[(5Z)-5-(5-bromo-2-oxo-1,2-dihydro-3H-indol-3-ylidene)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]butanedioic acid
N-[(1S)-2-AMINO-1-(2,4-DICHLOROBENZYL)ETHYL]-5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]THIOPHENE-2-CARBOXAMIDE
C15 H9 Br N2 O6 S2
QGNRETMYLHRUBB-OZEWEUHLSA-N
 Ligand Interaction
Z88
Query on Z88

Download SDF File 
Download CCD File 
A, B
N-[(4-bromophenyl)sulfonyl]acetamide
C8 H8 Br N O3 S
GUSSBUVTIMQOBB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Z89Ki: 147000 nM BINDINGMOAD
Z89Kd: 138000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.712α = 90.00
b = 38.611β = 114.70
c = 78.817γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance