7Q7V

Crystal structure of human BCL6 BTB domain in complex with compound 12a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Optimizing Shape Complementarity Enables the Discovery of Potent Tricyclic BCL6 Inhibitors.

Davis, O.A.Cheung, K.J.Brennan, A.Lloyd, M.G.Rodrigues, M.J.Pierrat, O.A.Collie, G.W.Le Bihan, Y.V.Huckvale, R.Harnden, A.C.Varela, A.Bright, M.D.Eve, P.Hayes, A.Henley, A.T.Carter, M.D.McAndrew, P.C.Talbot, R.Burke, R.van Montfort, R.L.M.Raynaud, F.I.Rossanese, O.W.Meniconi, M.Bellenie, B.R.Hoelder, S.

(2022) J Med Chem 65: 8169-8190

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02174
  • Primary Citation of Related Structures:  
    7Q7R, 7Q7S, 7Q7T, 7Q7U, 7Q7V

  • PubMed Abstract: 

    To identify new chemical series with enhanced binding affinity to the BTB domain of B-cell lymphoma 6 protein, we targeted a subpocket adjacent to Val18. With no opportunities for strong polar interactions, we focused on attaining close shape complementarity by ring fusion onto our quinolinone lead series. Following exploration of different sized rings, we identified a conformationally restricted core which optimally filled the available space, leading to potent BCL6 inhibitors. Through X-ray structure-guided design, combined with efficient synthetic chemistry to make the resulting novel core structures, a >300-fold improvement in activity was obtained by the addition of seven heavy atoms.


  • Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, U.K..


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein144Homo sapiensMutation(s): 0 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9GR (Subject of Investigation/LOI)
Query on 9GR

Download Ideal Coordinates CCD File 
B [auth A]2-chloranyl-4-[[(2R)-2-cyclopropyl-7-methyl-6-oxidanylidene-1,2,3,4-tetrahydro-[1,4]oxazepino[2,3-c]quinolin-10-yl]amino]pyridine-3-carbonitrile
C22 H20 Cl N5 O2
YYUZEYWEXPZHOG-MRXNPFEDSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9GR BindingDB:  7Q7V IC50: min: 38.9, max: 670 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.307α = 90
b = 67.307β = 90
c = 166.807γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A11566

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description