Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.77 kDa 
• Atom Count: 2854 
• Modelled Residue Count: 328 
• Deposited Residue Count: 360 
• Unique protein chains: 1

5N68

Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9m

• PDB DOI: 10.2210/pdb5N68/pdb

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


• Deposited: 2017-02-14 Released: 2017-09-20 
• Deposition Author(s): Buehrmann, M., Mueller, M.P., Rauh, D.
• Funding Organization(s): German Federal Ministry for Education and Research (NGFNPlus and e:Med)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.220 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Literature

Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38 alpha MAPK.

Buhrmann, M., Wiedemann, B.M., Muller, M.P., Hardick, J., Ecke, M., Rauh, D.

(2017) PLoS One 12: e0184627-e0184627

• PubMed: 28892510 
• DOI: 10.1371/journal.pone.0184627
• Primary Citation of Related Structures:  
  5N63, 5N64, 5N65, 5N66, 5N67, 5N68


• PubMed Abstract: 
  

In protein kinase research, identifying and addressing small molecule binding sites other than the highly conserved ATP-pocket are of intense interest because this line of investigation extends our understanding of kinase function beyond the catalytic phosphotransfer. Such alternative binding sites may be involved in altering the activation state through subtle conformational changes, control cellular enzyme localization, or in mediating and disrupting protein-protein interactions. Small organic molecules that target these less conserved regions might serve as tools for chemical biology research and to probe alternative strategies in targeting protein kinases in disease settings. Here, we present the structure-based design and synthesis of a focused library of 2-arylquinazoline derivatives to target the lipophilic C-terminal binding pocket in p38α MAPK, for which a clear biological function has yet to be identified. The interactions of the ligands with p38α MAPK was analyzed by SPR measurements and validated by protein X-ray crystallography.

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Organizational Affiliation: 

Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8OK	B [auth A]	2-(4-morpholin-4-ylphenyl)-~{N}4-(2-phenylethyl)quinazoline-4,7-diamine C26 H27 N5 O WGLAXIALKDLESY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.220 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.24	α = 90
b = 74.98	β = 90
c = 78.86	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-14 
• Released Date: 2017-09-20 
Deposition Author(s): Buehrmann, M., Mueller, M.P., Rauh, D.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research (NGFNPlus and e:Med)	Germany	BMBF 01GS08104, 01ZX1303C

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection