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: 42.33 kDa 
• Atom Count: 2963 
• Residue Count: 338 
• Unique protein chains: 1

3GCV

Human P38 MAP Kinase in Complex with RL62

• DOI: 10.2210/pdb3GCV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-22 Released: 2009-06-09 
• Deposition Author(s): Gruetter, C., Simard, J.R., Getlik, M., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.254 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Development of a fluorescent-tagged kinase assay system for the detection and characterization of allosteric kinase inhibitors.

Simard, J.R., Getlik, M., Grutter, C., Pawar, V., Wulfert, S., Rabiller, M., Rauh, D.

(2009) J Am Chem Soc 131: 13286-13296

• PubMed: 19572644 
• DOI: 10.1021/ja902010p
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Kinase disregulation disrupts the intricate network of intracellular signaling pathways and contributes to the onset of diseases such as cancer. Although several kinase inhibitors are on the market, inhibitor selectivity and drug resistance mutations persist as fundamental challenges in the development of effective long-term treatments. Chemical entities binding to less conserved allosteric sites would be expected to offer new opportunities for scaffold development. Because no high-throughput method was previously available, we developed a fluorescence-based kinase binding assay for identifying and characterizing ligands which stabilize the inactive kinase conformation. Here, we present a description of the development and validation of this assay using the serine/threonine kinase p38alpha. By covalently attaching fluorophores to the activation loop of the kinase, we were able to detect conformational changes and measure the K(d), k(on), and k(off) associated with the binding and dissociation of ligands to the allosteric pocket. We report the SAR of a synthesized focused library of pyrazolourea derivatives, a scaffold known to bind with high affinity to the allosteric pocket of p38alpha. Additionally, we used protein X-ray crystallography together with our assay to examine the binding and dissociation kinetics to characterize potent quinazoline- and quinoline-based type II inhibitors, which also utilize this binding pocket in p38alpha. Last, we identified the b-Raf inhibitor sorafenib as a potent low nanomolar inhibitor of p38alpha and used protein X-ray crystallography to confirm a unique binding mode to the inactive kinase conformation.

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Organizational Affiliation: 

Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 4  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens) Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539 GTEx  ENSG00000112062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SS6	A	1-{3-[(6-aminoquinazolin-4-yl)amino]phenyl}-3-[3-tert-butyl-1-(3-methylphenyl)-1H-pyrazol-5-yl]urea C29 H30 N8 O MWDKKNFEOXEAEC-UHFFFAOYSA-N
BOG	A	B-OCTYLGLUCOSIDE C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SS6	Kd :  74   nM  PDBBind
SS6	Kd:  74   nM  Binding MOAD
SS6	IC50:  320   nM  BindingDB
SS6	IC50:  420   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.254 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.785	α = 90
b = 70.003	β = 90
c = 74.513	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-22 
• Released Date: 2009-06-09 
Deposition Author(s): Gruetter, C., Simard, J.R., Getlik, M., Rauh, D.

Revision History 

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance