8PT9

JNK1 covalently bound to BD838 cyclohexenone based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8PT9/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.225 
• R-Value Work: 0.206 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Tunable c-Jun N-terminal kinase (JNK) inhibitors that target a specific cysteine by a reversible covalent bond

Sok, P., Poti, A., Balint, D., Remenyi, A., Soos, T.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 127.88 kDa 
• Atom Count: 8,391 
• Modelled Residue Count: 1,056 
• Deposited Residue Count: 1,098 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 8	A, B, C	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DVI (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	methyl (1S,3S)-1-methyl-3-[[3-[[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]carbamoyl]-4-oxidanylidene-cyclohexane-1-carboxylate C33 H32 N6 O5 LOKFZRXMKAWKTK-JQJBXXCASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.225 
• R-Value Work: 0.206 
• R-Value Observed: 0.215 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.552	α = 90
b = 106.552	β = 90
c = 99.795	γ = 120

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: 2024-07-24 
Deposition Author(s): Sok, P., Poti, A., Remenyi, A.

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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: 2024-10-09
  Changes: Structure summary