6ZZ1

Crystal structure of MLKL executioner domain in complex with a covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Locking mixed-lineage kinase domain-like protein in its auto-inhibited state prevents necroptosis.

Rubbelke, M.Fiegen, D.Bauer, M.Binder, F.Hamilton, J.King, J.Thamm, S.Nar, H.Zeeb, M.

(2020) Proc Natl Acad Sci U S A 117: 33272-33281

  • DOI: https://doi.org/10.1073/pnas.2017406117
  • Primary Citation of Related Structures:  
    6ZLE, 6ZPR, 6ZVO, 6ZZ1

  • PubMed Abstract: 

    As an alternative pathway of controlled cell death, necroptosis can be triggered by tumor necrosis factor via the kinases RIPK1/RIPK3 and the effector protein mixed-lineage kinase domain-like protein (MLKL). Upon activation, MLKL oligomerizes and integrates into the plasma membrane via its executioner domain. Here, we present the X-ray and NMR costructures of the human MLKL executioner domain covalently bound via Cys86 to a xanthine class inhibitor. The structures reveal that the compound stabilizes the interaction between the auto-inhibitory brace helix α6 and the four-helix bundle by stacking to Phe148. An NMR-based functional assay observing the conformation of this helix showed that the F148A mutant is unresponsive to the compound, providing further evidence for the importance of this interaction. Real-time and diffusion NMR studies demonstrate that xanthine derivatives inhibit MLKL oligomerization. Finally, we show that the other well-known MLKL inhibitor Necrosulfonamide, which also covalently modifies Cys86, must employ a different mode of action.


  • Organizational Affiliation

    Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mixed lineage kinase domain-like protein
A, B
153Homo sapiensMutation(s): 0 
Gene Names: MLKL
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB16 (Homo sapiens)
Explore Q8NB16 
Go to UniProtKB:  Q8NB16
PHAROS:  Q8NB16
GTEx:  ENSG00000168404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NB16
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QOK (Subject of Investigation/LOI)
Query on QOK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
7-(2-methoxyethoxymethyl)-1,3-dimethyl-purine-2,6-dione
C11 H16 N4 O4
BSIZPWZVMIVPIN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.709α = 90
b = 56.709β = 90
c = 90.501γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
DIMPLEphasing
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-01-06
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description