8R5F | pdb_00008r5f

ERK2 covalently bound to RU83 cyclohexenone based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8R5F/pdb

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


• Deposited: 2023-11-16 Released: 2024-11-27 
• Deposition Author(s): Sok, P., Poti, A., Remenyi, A.
• Funding Organization(s): Hungarian National Research, Development and Innovation Office

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.218 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

The covalent coordination of cyclohexenone inhibitors in the MAP kinase docking groove

Poti, A., Sok, P., Remenyi, A.

To be published.

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: 42.64 kDa 
• Atom Count: 2,960 
• Modeled Residue Count: 337 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Y3H (Subject of Investigation/LOI)	D [auth A]	~{O}3-~{tert}-butyl ~{O}1-prop-2-ynyl (1~{S},3~{S})-1-methyl-4-oxidanylidene-cyclohexane-1,3-dicarboxylate C16 H22 O5 VWWMPCGCVQSEOW-ZBEGNZNMSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.218 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.486	α = 90
b = 77.081	β = 90
c = 123.251	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Sok, P., Poti, A., Remenyi, A.

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Funding Organization	Location	Grant Number
Hungarian National Research, Development and Innovation Office	Hungary	KKP 126963

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release