7Q7V | pdb_00007q7v

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

• PDB DOI: https://doi.org/10.2210/pdb7Q7V/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-11-09 Released: 2022-06-15 
• Deposition Author(s): Rodrigues, M.J., Le Bihan, Y.-V., van Montfort, R.L.M.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.206 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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

• PubMed: 35657291 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c02174
• Primary Citation 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.

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Organizational Affiliation: 
• Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, U.K..
Division of Structural Biology, The Institute of Cancer Research, London SM2 5NG, U.K..

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.12 kDa 
• Atom Count: 1,209 
• Modeled Residue Count: 131 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A	144	Homo sapiens	Mutation(s): 0  Gene Names: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens) Explore P41182  Go to UniProtKB:  P41182
PHAROS:  P41182 GTEx:  ENSG00000113916

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9GR (Subject of Investigation/LOI)	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	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9GR	BindingDB:  7Q7V	IC50: min: 38.9, max: 210 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.206 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.307	α = 90
b = 67.307	β = 90
c = 166.807	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Rodrigues, M.J., Le Bihan, Y.-V., van Montfort, R.L.M.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C309/A11566

Revision History  

• 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