Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 41.95 kDa 
• Atom Count: 2803 
• Residue Count: 336 
• Unique protein chains: 1

4DLJ

Human p38 MAP kinase in complex with RL163

• DOI: 10.2210/pdb4DLJ/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-06 Released: 2013-01-23 
• Deposition Author(s): Gruetter, C., Termathe, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.314 
• R-Value Work: 0.209 
• R-Value Observed: 0.216 

Literature

Fluorophore labeled kinase detects ligands that bind within the MAPK insert of p38alpha kinase.

Getlik, M., Simard, J.R., Termathe, M., Grutter, C., Rabiller, M., van Otterlo, W.A., Rauh, D.

(2012) PLoS One 7: e39713-e39713

• PubMed: 22768308 
• DOI: 10.1371/journal.pone.0039713
• Primary Citation of Related Structures:  
  4DLI, 4DLJ


• PubMed Abstract: 
  

The vast majority of small molecules known to modulate kinase activity, target the highly conserved ATP-pocket. Consequently, such ligands are often less specific and in case of inhibitors, this leads to the inhibition of multiple kinases. Thus, selective modulation of kinase function remains a major hurdle. One of the next great challenges in kinase research is the identification of ligands which bind to less conserved sites and target the non-catalytic functions of protein kinases. However, approaches that allow for the unambiguous identification of molecules that bind to these less conserved sites are few in number. We have previously reported the use of fluorescent labels in kinases (FLiK) to develop direct kinase binding assays that exclusively detect ligands which stabilize inactive (DFG-out) kinase conformations. Here, we present the successful application of the FLiK approach to develop a high-throughput binding assay capable of directly monitoring ligand binding to a remote site within the MAPK insert of p38α mitogen-activated protein kinase (MAPK). Guided by the crystal structure of an initially identified hit molecule in complex with p38α, we developed a tight binding ligand which may serve as an ideal starting point for further investigations of the biological function of the MAPK insert in regulating the p38α signaling pathway.

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Organizational Affiliation: 

Chemical Genomics Centre of the Max Planck Society, 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
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539 GTEx  ENSG00000112062

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6RG	A	2-phenyl-N~4~-(2-phenylethyl)quinazoline-4,7-diamine C22 H20 N4 TZGHZEALSHYAJC-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
6RG	Kd :  1200   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.314 
• R-Value Work: 0.209 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.98	α = 90
b = 74.51	β = 90
c = 78.32	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-06 
• Released Date: 2013-01-23 
Deposition Author(s): Gruetter, C., Termathe, M.

Revision History 

• Version 1.0: 2013-01-23
  Type: Initial release