8PSW | pdb_00008psw

ERK2 covalently bound to RU67 cyclohexenone based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8PSW/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-13 Released: 2024-07-24 
• Deposition Author(s): Sok, P., Poti, A., Remenyi, A., Gogl, G.
• Funding Organization(s): National Research Development and Innovation Office (NKFIH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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

• PubMed: 39366929 
• DOI: https://doi.org/10.1038/s41467-024-52574-1
• Primary Citation 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.

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Organizational Affiliation: 
• Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.
Doctoral School of Biology, Eötvös Loránd University, Budapest, Hungary.
Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.
Hevesy György PhD School of Chemistry, Eötvös Loránd University, Budapest, Hungary.
NMR Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, Budapest, Hungary.
Department of Organic Chemistry, University of Debrecen, Debrecen, Hungary.
MS Metabolomic Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, Budapest, Hungary.
Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary. [e-mail].
Biomolecular Interaction Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 42.52 kDa 
• Atom Count: 2,912 
• Modeled Residue Count: 338 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	364	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1, PRKM2 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AN2	B [auth A]	AMP PHOSPHORAMIDATE C10 H16 N6 O9 P2 FQMDCEJHLOLKLI-KQYNXXCUSA-N
D2I (Subject of Investigation/LOI)	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 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.47	α = 90
b = 77.39	β = 90
c = 127.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Sok, P., Poti, A., Remenyi, A., Gogl, G.

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Funding Organization	Location	Grant Number
National Research Development and Innovation Office (NKFIH)	Hungary	KKP 126963

Revision History  

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