9R59 | pdb_00009r59

Crystal structure of MAPKAPK2 with a covalent compound GCL334 targeting lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.229 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

A twist in the tale: shifting from covalent targeting of a tyrosine in JAK3 to a lysine in MK2.

Hillebrand, L.Wang, G.Rasch, A.Masberg, B.Chaikuad, A.Kronenberger, T.Gunther, E.Forster, M.Poso, A.Lammerhofer, M.Laufer, S.A.Knapp, S.Gehringer, M.

(2025) RSC Med Chem 16: 4906-4919

  • DOI: https://doi.org/10.1039/d5md00440c
  • Primary Citation of Related Structures:  
    9R59, 9R5Z

  • PubMed Abstract: 

    While cysteine targeting in kinases is well established and widely used, covalent interactions with other amino acids remain much less explored. We aimed to develop covalent inhibitors targeting tyrosine residues in the protein kinases JAK3 and MK2 using structure-based design principles to generate small sets of ligands containing tyrosine-reactive sulfonyl fluoride and the less-explored fluorosulfate warheads. While the JAK3 inhibitors failed to achieve covalent binding, the fluorosulfate-bearing MK2 inhibitor 42, which had been designed as an allosteric binder, unexpectedly formed a bond with the "catalytic" lysine, additionally uncovering a unique interaction at the hinge region. This highlights the untapped potential of fluorosulfates and provides a rare example of the use of this electrophile for lysine targeting in kinases. Our results highlight the limitations of traditional design methods and support the integration of fragment/lead-like covalent library screening to discover unanticipated interactions.


  • Organizational Affiliation
    • Faculty of Medicine, Institute of Biomedical Engineering, Department for Medicinal Chemistry, Eberhard Karls University Tübingen Auf der Morgenstelle 8 D-72076 Tübingen Germany matthias.gehringer@uni-tuebingen.de.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2320Homo sapiensMutation(s): 0 
Gene Names: MAPKAPK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49137 (Homo sapiens)
Explore P49137 
Go to UniProtKB:  P49137
PHAROS:  P49137
GTEx:  ENSG00000162889 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49137
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JH4 (Subject of Investigation/LOI)
Query on A1JH4

Download Ideal Coordinates CCD File 
B [auth A]5-[3-[bis(oxidanyl)-$l^{3}-sulfanyl]oxy-4-chloranyl-phenyl]-~{N}-(4-piperazin-1-ylphenyl)-~{N}-(pyridin-2-ylmethyl)furan-2-carboxamide
C27 H27 Cl N4 O6 S
OYYFNINEAKHFQQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.229 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.745α = 90
b = 102.745β = 90
c = 167.683γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Structural Genomics Consortium (SGC)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Database references
  • Version 1.2: 2025-10-22
    Changes: Database references