6CQ1 | pdb_00006cq1

BCL6 BTB domain in complex with 15a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6CQ1

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.

Cheng, H.Linhares, B.M.Yu, W.Cardenas, M.G.Ai, Y.Jiang, W.Winkler, A.Cohen, S.Melnick, A.MacKerell Jr., A.Cierpicki, T.Xue, F.

(2018) J Med Chem 61: 7573-7588

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00040
  • Primary Citation Related Structures: 
    6C3L, 6C3N, 6CQ1

  • PubMed Abstract: 

    Protein-protein interactions (PPI) between the transcriptional repressor B-cell lymphoma 6 (BCL6) BTB domain (BCL6 BTB ) and its corepressors have emerged as a promising target for anticancer therapeutics. However, identification of potent, drug-like inhibitors of BCL6 BTB has remained challenging. Using NMR-based screening of a library of fragment-like small molecules, we have identified a thiourea compound (7CC5) that binds to BCL6 BTB . From this hit, the application of computer-aided drug design (CADD), medicinal chemistry, NMR spectroscopy, and X-ray crystallography has yielded an inhibitor, 15f, that demonstrated over 100-fold improved potency for BCL6 BTB . This gain in potency was achieved by a unique binding mode that mimics the binding mode of the corepressor SMRT in the aromatic and the HDCH sites. The structure-activity relationship based on these new inhibitors will have a significant impact on the rational design of novel BCL6 inhibitors, facilitating the identification of therapeutics for the treatment of BCL6-dependent tumors.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States.

Macromolecule Content 

  • Total Structure Weight: 30.92 kDa 
  • Atom Count: 2,306 
  • Modeled Residue Count: 246 
  • Deposited Residue Count: 262 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein
A, B
131Homo sapiensMutation(s): 4 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F8J

Query on F8J



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2-{6-({[2-(1H-indol-3-yl)ethyl]carbamothioyl}amino)-3-[(4-methylpiperazin-1-yl)methyl]-1H-indol-1-yl}-N-(propan-2-yl)acetamide
C30 H39 N7 O S
DCSGGGDRUYCRAM-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
F8J BindingDB:  6CQ1 Kd: 2.19e+5 (nM) from 1 assay(s)
IC50: 1.42e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.012α = 83.654
b = 39.621β = 73.633
c = 55.225γ = 66.98
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description