8C78

Crystal structure of human BCL6 BTB domain in complex with compound CCT374705


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Discovery of an In Vivo Chemical Probe for BCL6 Inhibition by Optimization of Tricyclic Quinolinones.

Harnden, A.C.Davis, O.A.Box, G.M.Hayes, A.Johnson, L.D.Henley, A.T.de Haven Brandon, A.K.Valenti, M.Cheung, K.J.Brennan, A.Huckvale, R.Pierrat, O.A.Talbot, R.Bright, M.D.Akpinar, H.A.Miller, D.S.J.Tarantino, D.Gowan, S.de Klerk, S.McAndrew, P.C.Le Bihan, Y.V.Meniconi, M.Burke, R.Kirkin, V.van Montfort, R.L.M.Raynaud, F.I.Rossanese, O.W.Bellenie, B.R.Hoelder, S.

(2023) J Med Chem 66: 5892-5906

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00155
  • Primary Citation of Related Structures:  
    8C78

  • PubMed Abstract: 

    B-cell lymphoma 6 (BCL6) is a transcriptional repressor and oncogenic driver of diffuse large B-cell lymphoma (DLBCL). Here, we report the optimization of our previously reported tricyclic quinolinone series for the inhibition of BCL6. We sought to improve the cellular potency and in vivo exposure of the non-degrading isomer, CCT373567 , of our recently published degrader, CCT373566 . The major limitation of our inhibitors was their high topological polar surface areas (TPSA), leading to increased efflux ratios. Reducing the molecular weight allowed us to remove polarity and decrease TPSA without considerably reducing solubility. Careful optimization of these properties, as guided by pharmacokinetic studies, led to the discovery of CCT374705 , a potent inhibitor of BCL6 with a good in vivo profile. Modest in vivo efficacy was achieved in a lymphoma xenograft mouse model after oral dosing.


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
TWI (Subject of Investigation/LOI)
Query on TWI

Download Ideal Coordinates CCD File 
B [auth A](2~{S})-10-[(3-chloranyl-2-fluoranyl-pyridin-4-yl)amino]-2-cyclopropyl-3,3-bis(fluoranyl)-7-methyl-2,4-dihydro-1~{H}-[1,4]oxazepino[2,3-c]quinolin-6-one
C21 H18 Cl F3 N4 O2
MCRHRRIGPAVFNY-SFHVURJKSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.588α = 90
b = 67.588β = 90
c = 167.162γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

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: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 2.0: 2023-05-24
    Changes: Non-polymer description