7QK0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Improved Binding Affinity and Pharmacokinetics Enable Sustained Degradation of BCL6 In Vivo .

Huckvale, R.Harnden, A.C.Cheung, K.J.Pierrat, O.A.Talbot, R.Box, G.M.Henley, A.T.de Haven Brandon, A.K.Hallsworth, A.E.Bright, M.D.Akpinar, H.A.Miller, D.S.J.Tarantino, D.Gowan, S.Hayes, A.Gunnell, E.A.Brennan, A.Davis, O.A.Johnson, L.D.de Klerk, S.McAndrew, 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.

(2022) J Med Chem 65: 8191-8207

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02175
  • Primary Citation of Related Structures:  
    7QK0

  • PubMed Abstract: 

    The transcriptional repressor BCL6 is an oncogenic driver found to be deregulated in lymphoid malignancies. Herein, we report the optimization of our previously reported benzimidazolone molecular glue-type degrader CCT369260 to CCT373566 , a highly potent probe suitable for sustained depletion of BCL6 in vivo . We observed a sharp degradation SAR, where subtle structural changes conveyed the ability to induce degradation of BCL6. CCT373566 showed modest in vivo efficacy in a lymphoma xenograft mouse model following oral dosing.


  • 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EBL (Subject of Investigation/LOI)
Query on EBL

Download Ideal Coordinates CCD File 
B [auth A](2~{S})-10-[[5-chloranyl-2-[(3~{S},5~{R})-3-methyl-5-oxidanyl-piperidin-1-yl]pyrimidin-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
C26 H29 Cl F2 N6 O3
GSGDUDAFETZSPM-IATAILRESA-N
DMS
Query on DMS

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.839α = 90
b = 66.839β = 90
c = 167.279γ = 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