3LBZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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
  • Primary Citation of Related Structures:  
    3LBZ

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B-cell lymphoma 6 proteinAB127Homo sapiensMutation(s): 3 
Gene Names: BCL5BCL6LAZ3ZBTB27ZNF51
Find proteins for P41182 (Homo sapiens)
Explore P41182 
Go to UniProtKB:  P41182
NIH Common Fund Data Resources
PHAROS  P41182
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z89
Query on Z89

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
C15 H9 Br N2 O6 S2
QGNRETMYLHRUBB-OZEWEUHLSA-N
 Ligand Interaction
Z88
Query on Z88

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  Binding MOAD
Z89Kd :  138000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.712α = 90
b = 38.611β = 114.7
c = 78.817γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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