9Q03 | pdb_00009q03

Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of Potent and Selective BCL6 Ligand-Directed Degrader (LDD), BCL6-760.

Shunatona, H.P.Holmberg Douglas, N.Rhodes, J.Thomas, W.Da Silva, D.Gamez, J.Groza, M.Christoforou, A.Zhu, J.Johnson, S.Dodd, D.Huang, D.Griffin, J.Miseo, G.Whitefield, B.Weiss, D.Rader, J.Kuzu, E.Leisten, J.Del Rosario, J.Shi, L.Matyskiela, M.Chamberlain, P.P.Belmont, P.Alexander, M.Zapf, C.W.Groocock, L.Mortensen, D.S.

(2025) J Med Chem 68: 21502-21519

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01645
  • Primary Citation of Related Structures:  
    9Q03

  • PubMed Abstract: 

    The discovery of a potent and selective BCL6 ligand-directed degrader (LDD), BCL6-760 ( 45 ) is described. Through structure-activity relationships, the most potent heterobifunctional degraders of BCL6 were found to be those containing short aminopiperidine linkers in combination with an indazole-based cereblon (CRBN)-binding moiety (CBM). In vitro ADME profiling of potent molecules identified BCL6-760 as an ideal molecule for use in in vivo experiments due to its good passive permeability, solubility, and microsomal stability. Mechanistic studies confirmed that BCL6 degradation is CRBN mediated, and proteomic assessment indicates a clean and selective degradation profile. BCL6-760 exhibited good oral mouse PK and was capable of penetrant and sustained PD effects. At 60 mg/kg BID dosing, BCL6-760 achieves >90% BCL6 reduction and leads to an overall 64% tumor volume reduction in an OCI-LY-1 mouse xenograft efficacy model.


  • Organizational Affiliation
    • Bristol Myers Squibb, 10300 Campus Point Dr. Suite 100, San Diego, California 92121, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein
A, B
143Homo 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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon467Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
GTEx:  ENSG00000113851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CM7 (Subject of Investigation/LOI)
Query on A1CM7

Download Ideal Coordinates CCD File 
E [auth C](3R)-3-(6-{4-[(5-chloro-4-{[3-(3-hydroxy-3-methylbutyl)-1-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-5-yl]amino}pyrimidin-2-yl)(methyl)amino]piperidin-1-yl}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione
C36 H43 Cl N10 O4
UAPMBWAZZWBDFF-RUZDIDTESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Data collection, Database references