9MZA | pdb_00009mza

Chemically Hijacked BCL6-TCIP3-p300 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.277 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.245 (DCC) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A Bivalent Molecular Glue Linking Lysine Acetyltransferases to Oncogene-induced Cell Death.

Nix, M.N.Gourisankar, S.Sarott, R.C.Dwyer, B.G.Nettles, S.A.Martinez, M.M.Abuzaid, H.Yang, H.Wang, Y.Simanauskaite, J.M.Romero, B.A.Jones, H.M.Krokhotin, A.Lowensohn, T.N.Chen, L.Low, C.Davis, M.M.Fernandez, D.Zhang, T.Green, M.R.Hinshaw, S.M.Gray, N.S.Crabtree, G.R.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.03.14.643404
  • Primary Citation of Related Structures:  
    9MZA

  • PubMed Abstract: 

    Developing cancer therapies that induce robust death of the malignant cell is critical to prevent relapse. Highly effective strategies, such as immunotherapy, exemplify this observation. Here we provide the structural and molecular underpinnings for an approach that leverages chemical induced proximity to produce specific cell killing of diffuse large B cell lymphoma, the most common non-Hodgkin's lymphoma. We develop KAT-TCIPs (lysine acetyltransferase transcriptional/epigenetic chemical inducers of proximity) that redirect p300 and CBP to activate programmed cell death genes normally repressed by the oncogenic driver, BCL6. Acute treatment rapidly reprograms the epigenome to initiate apoptosis and repress c-MYC. The crystal structure of the chemically induced p300-BCL6 complex reveals how chance interactions between the two proteins can be systematically exploited to produce the exquisite potency and selectivity of KAT-TCIPs. Thus, the malignant function of an oncogenic driver can be co-opted to activate robust cell death, with implications for precision epigenetic therapies.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein
A, C
128Homo 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
Histone acetyltransferase p300
B, D
145Homo sapiensMutation(s): 0 
Gene Names: EP300P300
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens)
Explore Q09472 
Go to UniProtKB:  Q09472
PHAROS:  Q09472
GTEx:  ENSG00000100393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09472
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BUC (Subject of Investigation/LOI)
Query on A1BUC

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
1-{1-[5-({1-[5-chloro-4-({8-methoxy-1-methyl-3-[2-(methylamino)-2-oxoethoxy]-2-oxo-1,2-dihydroquinolin-6-yl}amino)pyrimidin-2-yl]piperidine-4-carbonyl}amino)pentanoyl]piperidin-4-yl}-3-[(6M)-7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl]-N-methyl-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide
C56 H68 Cl F2 N15 O7
GWSPREFNOSPUJZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.277 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.245 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.388α = 90
b = 94.79β = 90
c = 97.616γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R01CA276167-02

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release