8R5E | pdb_00008r5e

JNK1 covalently bound to RU77 cyclohexenone based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8R5E/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• 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: 1.70 Å
• R-Value Free: 
  0.222 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.177 (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: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 42.95 kDa 
• Atom Count: 3,044 
• Modeled Residue Count: 359 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 8	A	366	Homo sapiens	Mutation(s): 1  Gene Names: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens) Explore P45983  Go to UniProtKB:  P45983
PHAROS:  P45983 GTEx:  ENSG00000107643

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Y6K (Subject of Investigation/LOI)	D [auth A]	~{O}3-~{tert}-butyl ~{O}1-methyl (1~{S},3~{R},5~{R})-6-methylidene-4-oxidanylidene-bicyclo[3.2.1]octane-1,3-dicarboxylate C16 H22 O5 ILHZGEBKECHEND-UVWXRNBGSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.222 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.341	α = 90
b = 75.249	β = 90
c = 82.869	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
STARANISO	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