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: 41.96 kDa 
• Atom Count: 2817 
• Residue Count: 330 
• Unique protein chains: 1

3HV7

Human p38 MAP Kinase in Complex with RL38

• DOI: 10.2210/pdb3HV7/pdb

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


• Deposited: 2009-06-15 Released: 2009-11-17 
• Deposition Author(s): Gruetter, C., Simard, J.R., Getlik, M., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.203 
• R-Value Observed: 0.208 

Literature

Displacement assay for the detection of stabilizers of inactive kinase conformations.

Kluter, S., Grutter, C., Naqvi, T., Rabiller, M., Simard, J.R., Pawar, V., Getlik, M., Rauh, D.

(2010) J Med Chem 53: 357-367

• PubMed: 19928858 
• DOI: 10.1021/jm901297e
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Targeting protein kinases with small molecules outside the highly conserved ATP pocket to stabilize inactive kinase conformations is becoming a more desirable approach in kinase inhibitor research, since these molecules have advanced pharmacological properties compared to compounds exclusively targeting the ATP pocket. Traditional screening approaches for kinase inhibitors are often based on enzyme activity, but they may miss inhibitors that stabilize inactive kinase conformations by enriching the active state of the kinase. Here we present the development of a kinase binding assay employing a pyrazolourea type III inhibitor and enzyme fragment complementation (EFC) technology that is suitable to screen stabilizers of enzymatically inactive kinases. To validate this assay system, we report the binding characteristics of a series of kinase inhibitors to inactive p38alpha and JNK2. Additionally, we present protein X-ray crystallography studies to examine the binding modes of potent quinoline-based DFG-out binders in p38alpha.

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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): 0  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
1AU	A	1-[1-(3-aminophenyl)-3-tert-butyl-1H-pyrazol-5-yl]-3-naphthalen-1-ylurea C24 H25 N5 O HJWMLCDGRWWLAQ-UHFFFAOYSA-N
BOG	A	B-OCTYLGLUCOSIDE C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1AU	IC50:  90   nM  Binding MOAD
1AU	Kd :  12   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.279 
• R-Value Work: 0.203 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.71	α = 90
b = 74.52	β = 90
c = 78.91	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-15 
• Released Date: 2009-11-17 
Deposition Author(s): Gruetter, C., Simard, J.R., Getlik, M., Rauh, D.

Revision History 

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance