6EMH | pdb_00006emh

Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6EMH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-02 Released: 2018-08-08 
• Deposition Author(s): Macedo, J.T., Stehle, T., Blaum, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.261 (DCC) 

Starting Model: experimental

Literature

Structural Optimization of a Pyridinylimidazole Scaffold: Shifting the Selectivity from p38 alpha Mitogen-Activated Protein Kinase to c-Jun N-Terminal Kinase 3.

Ansideri, F., Macedo, J.T., Eitel, M., El-Gokha, A., Zinad, D.S., Scarpellini, C., Kudolo, M., Schollmeyer, D., Boeckler, F.M., Blaum, B.S., Laufer, S.A., Koch, P.

(2018) ACS Omega 3: 7809-7831

• PubMed: 30087925 
• DOI: https://doi.org/10.1021/acsomega.8b00668
• Primary Citation Related Structures: 
  6EKD, 6EMH, 6EQ9


• PubMed Abstract: 
  

  Starting from known p38α mitogen-activated protein kinase (MAPK) inhibitors, a series of inhibitors of the c-Jun N-terminal kinase (JNK) 3 was obtained. Altering the substitution pattern of the pyridinylimidazole scaffold proved to be effective in shifting the inhibitory activity from the original target p38α MAPK to the closely related JNK3. In particular, a significant improvement for JNK3 selectivity could be achieved by addressing the hydrophobic region I with a small methyl group. Furthermore, additional structural modifications permitted to explore structure-activity relationships. The most potent inhibitor 4-(4-methyl-2-(methylthio)-1 H -imidazol-5-yl)- N -(4-morpholinophenyl)pyridin-2-amine showed an IC ₅₀ value for the JNK3 in the low triple digit nanomolar range and its binding mode was confirmed by X-ray crystallography.

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Organizational Affiliation: 
• Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Interfaculty Institute of Biochemistry, Eberhard Karls Universität Tübingen, Hoppe-Seyler-Straße 4, 72076 Tübingen, Germany.
Department of Organic Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, D-55099 Mainz, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 172.2 kDa 
• Atom Count: 12,089 
• Modeled Residue Count: 1,353 
• Deposited Residue Count: 1,468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A, B, C, D	367	Homo sapiens	Mutation(s): 0  Gene Names: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens) Explore P53779  Go to UniProtKB:  P53779
PHAROS:  P53779 GTEx:  ENSG00000109339

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C15	J [auth A], N [auth B]	N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE C17 H38 N O3 S IZWSFJTYBVKZNK-UHFFFAOYSA-O
BGE (Subject of Investigation/LOI)	H [auth A], L [auth B], Q [auth C], V [auth D]	4-(4-methyl-1~{H}-imidazol-5-yl)-~{N}-(4-morpholin-4-ylphenyl)pyridin-2-amine C19 H21 N5 O KJQAULYFYNEAHK-UHFFFAOYSA-N
PEG	P [auth C], U [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	S [auth C], Y [auth D], Z [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	E [auth A], F [auth A], K [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	I [auth A], M [auth B], R [auth C], W [auth D], X [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A], O [auth C], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.261 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.56	α = 90
b = 114.26	β = 90
c = 157.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Macedo, J.T., Stehle, T., Blaum, B.S.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2018-08-22
  Changes: Data collection, Database references
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description