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: 42.38 kDa 
• Atom Count: 2851 
• Residue Count: 336 
• Unique protein chains: 1

3IW5

Human p38 MAP Kinase in Complex with an Indole Derivative

• DOI: 10.2210/pdb3IW5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-09-02 Released: 2009-11-17 
• Deposition Author(s): Gruetter, C., Simard, J.R., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.291 
• R-Value Work: 0.205 
• R-Value Observed: 0.211 

Literature

High-Throughput Screening To Identify Inhibitors Which Stabilize Inactive Kinase Conformations in p38alpha

Simard, J.R., Gruetter, C., Pawar, V., Aust, B., Wolf, A., Rabiller, M., Wulfert, S., Robubi, A., Kluter, S., Ottmann, C., Rauh, D.

(2009) J Am Chem Soc 131: 18478-18488

• PubMed: 19950957 
• DOI: 10.1021/ja907795q
• Primary Citation of Related Structures:  
  3IW5, 3IW6, 3IW7, 3IW8


• PubMed Abstract: 
  

Small molecule kinase inhibitors are an attractive means to modulate kinase activities in medicinal chemistry and chemical biology research. In the physiological setting of a cell, kinase function is orchestrated by a plethora of regulatory processes involving the structural transition of kinases between inactive and enzymatically competent conformations and vice versa. The development of novel kinase inhibitors is mainly fostered by high-throughput screening initiatives where the small molecule perturbation of the phosphorylation reaction is measured to identify inhibitors. Such setups require enzymatically active kinase preparations and present a risk of solely identifying classical ATP-competitive Type I inhibitors. Here we report the high-throughput screening of a library of approximately 35000 small organic molecules with an assay system that utilizes enzymatically inactive human p38alpha MAP kinase to detect stabilizers of the pharmacologically more desirable DFG-out conformation. We used protein X-ray crystallography to characterize the binding mode of hit compounds and reveal structural features which explain how these ligands stabilize and/or induce the DFG-out conformation. Lastly, we show that although some of the hit compounds were confirmed by protein X-ray crystallography, they were not detected in classic phosphorylation assays, thus validating the unique sensitivity of the assay system used in this study and highlighting the potential of screening with inactive kinase preparations.

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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	Image
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) Explore Q16539  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
DF3	A	N-[2-(3-{[2-(2,3-dihydro-1,4-benzodioxin-6-ylamino)-2-oxoethyl]sulfanyl}-1H-indol-1-yl)ethyl]-3-(trifluoromethyl)benzamide C28 H24 F3 N3 O4 S BNPQVUSGXCJYEF-UHFFFAOYSA-N
BOG	A	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DF3	Kd:  839   nM  Binding MOAD
DF3	Kd :  839   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.291 
• R-Value Work: 0.205 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.07	α = 90
b = 70.05	β = 90
c = 74.05	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-02 
• Released Date: 2009-11-17 
Deposition Author(s): Gruetter, C., Simard, J.R., Rauh, D.

Revision History 

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary