6TOK

Crystal structure of human BCL6 BTB domain in complex with compound 23d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

AchievingIn VivoTarget Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders.

Bellenie, B.R.Cheung, K.J.Varela, A.Pierrat, O.A.Collie, G.W.Box, G.M.Bright, M.D.Gowan, S.Hayes, A.Rodrigues, M.J.Shetty, K.N.Carter, M.Davis, O.A.Henley, A.T.Innocenti, P.Johnson, L.D.Liu, M.de Klerk, S.Le Bihan, Y.V.Lloyd, M.G.McAndrew, P.C.Shehu, E.Talbot, R.Woodward, H.L.Burke, R.Kirkin, V.van Montfort, R.L.M.Raynaud, F.I.Rossanese, O.W.Hoelder, S.

(2020) J Med Chem 63: 4047-4068

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b02076
  • Primary Citation of Related Structures:  
    6TOF, 6TOG, 6TOH, 6TOI, 6TOJ, 6TOK, 6TOL, 6TOM, 6TON, 6TOO

  • PubMed Abstract: 

    Deregulation of the transcriptional repressor BCL6 enables tumorigenesis of germinal center B-cells, and hence BCL6 has been proposed as a therapeutic target for the treatment of diffuse large B-cell lymphoma (DLBCL). Herein we report the discovery of a series of benzimidazolone inhibitors of the protein-protein interaction between BCL6 and its co-repressors. A subset of these inhibitors were found to cause rapid degradation of BCL6, and optimization of pharmacokinetic properties led to the discovery of 5-((5-chloro-2-((3 R ,5 S )-4,4-difluoro-3,5-dimethylpiperidin-1-yl)pyrimidin-4-yl)amino)-3-(3-hydroxy-3-methylbutyl)-1-methyl-1,3-dihydro-2 H -benzo[ d ]imidazol-2-one (CCT369260), which reduces BCL6 levels in a lymphoma xenograft mouse model following oral dosing.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein128Homo 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
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-TRP-VAL-ILE-PRO-ALA6synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NQT (Subject of Investigation/LOI)
Query on NQT

Download Ideal Coordinates CCD File 
C [auth A]5-[[5-chloranyl-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one
C22 H26 Cl N7 O2
UQSUWLFWPLYJIQ-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
P [auth A],
Q [auth A],
R [auth A],
S [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NQT BindingDB:  6TOK IC50: 260 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.594α = 90
b = 68.594β = 90
c = 168.727γ = 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: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description