8PSW

ERK2 covalently bound to RU67 cyclohexenone based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Targeting a key protein-protein interaction surface on mitogen-activated protein kinases by a precision-guided warhead scaffold.

Poti, A.L.Balint, D.Alexa, A.Sok, P.Ozsvath, K.Albert, K.Turczel, G.Magyari, S.Ember, O.Papp, K.Kiraly, S.B.Imre, T.Nemeth, K.Kurtan, T.Gogl, G.Varga, S.Soos, T.Remenyi, A.

(2024) Nat Commun 15: 8607-8607

  • DOI: https://doi.org/10.1038/s41467-024-52574-1
  • Primary Citation of Related Structures:  
    8PSR, 8PST, 8PSW, 8PSY, 8PT0, 8PT1, 8PT3, 8PT5

  • PubMed Abstract: 

    For mitogen-activated protein kinases (MAPKs) a shallow surface-distinct from the substrate binding pocket-called the D(ocking)-groove governs partner protein binding. Screening of broad range of Michael acceptor compounds identified a double-activated, sterically crowded cyclohexenone moiety as a promising scaffold. We show that compounds bearing this structurally complex chiral warhead are able to target the conserved MAPK D-groove cysteine via reversible covalent modification and interfere with the protein-protein interactions of MAPKs. The electronic and steric properties of the Michael acceptor can be tailored via different substitution patterns. The inversion of the chiral center of the warhead can reroute chemical bond formation with the targeted cysteine towards the neighboring, but less nucleophilic histidine. Compounds bind to the shallow MAPK D-groove with low micromolar affinity in vitro and perturb MAPK signaling networks in the cell. This class of chiral, cyclic and enhanced 3D shaped Michael acceptor scaffolds offers an alternative to conventional ATP-competitive drugs modulating MAPK signaling pathways.


  • Organizational Affiliation

    Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1364Homo sapiensMutation(s): 0 
Gene Names: MAPK1ERK2PRKM1PRKM2
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
PHAROS:  P28482
GTEx:  ENSG00000100030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28482
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AN2
Query on AN2

Download Ideal Coordinates CCD File 
B [auth A]AMP PHOSPHORAMIDATE
C10 H16 N6 O9 P2
FQMDCEJHLOLKLI-KQYNXXCUSA-N
D2I (Subject of Investigation/LOI)
Query on D2I

Download Ideal Coordinates CCD File 
C [auth A]~{O}3-~{tert}-butyl ~{O}1-methyl (1~{R},3~{R})-4-oxidanylidene-1-(phenylmethyl)cyclohexane-1,3-dicarboxylate
C20 H26 O5
WAKMFGLCJLDCIS-QRWLVFNGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.47α = 90
b = 77.39β = 90
c = 127.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Development and Innovation Office (NKFIH)HungaryKKP 126963

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary