7NM2

Solution structure of MLKL executioner domain in complex with a fragment


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Discovery and Structure-Based Optimization of Fragments Binding the Mixed Lineage Kinase Domain-like Protein Executioner Domain.

Rubbelke, M.Hamilton, J.Binder, F.Bauer, M.King, J.Nar, H.Zeeb, M.

(2021) J Med Chem 64: 15629-15638

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00686
  • Primary Citation of Related Structures:  
    7NM2, 7NM4, 7NM5

  • PubMed Abstract: 

    Necroptosis is a form of programmed cell death that in case of misregulation can lead to inflammatory diseases. Mixed lineage kinase domain-like protein (MLKL), the effector protein in the canonical necroptosis signaling pathway, becomes activated by phosphorylation. Here, we report the identification of novel reversible binders of the MLKL executioner domain by a protein NMR-detected fragment-based screen. Determination of protein fragment costructures using NMR spectroscopy revealed a small molecule binding site that is distinct from the previously identified binding site of covalent MLKL inhibitors. Affinity optimization of the initially prioritized hit with millimolar affinity was achieved by NMR-guided structure-based design and yielded fragment-like molecules with a K D of 50 μM. Furthermore, we demonstrate that the improved fragment competes for the same binding site as nonyl-maltoside, a detergent that in conjunction with phytic acid activates the MLKL executioner domain.


  • Organizational Affiliation

    Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 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 protein157Homo 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
UJ5 (Subject of Investigation/LOI)
Query on UJ5

Download Ideal Coordinates CCD File 
B [auth A]2-[(~{S})-methoxy-(4-propan-2-ylphenyl)methyl]-3~{H}-benzimidazole-5-carboxylic acid
C19 H20 N2 O3
PVZNGPPPFPTWEL-KRWDZBQOSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UJ5 BindingDB:  7NM2 Kd: min: 5.00e+4, max: 2.15e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-24
    Changes: Data collection, Database references
  • Version 1.3: 2023-06-14
    Changes: Other
  • Version 1.4: 2024-06-19
    Changes: Data collection, Database references