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: 30.74 kDa 
• Atom Count: 2284 
• Modelled Residue Count: 259 
• Deposited Residue Count: 266 
• Unique protein chains: 1

3MJ2

X-ray crystal structure of ITK complexed with inhibitor BMS-509744

• DOI: 10.2210/pdb3MJ2/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-04-12 Released: 2010-06-30 
• Deposition Author(s): Kuglstatter, A., Villasenor, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.252 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Crystal structures of IL-2-inducible T cell kinase complexed with inhibitors: insights into rational drug design and activity regulation.

Kutach, A.K., Villasenor, A.G., Lam, D., Belunis, C., Janson, C., Lok, S., Hong, L.N., Liu, C.M., Deval, J., Novak, T.J., Barnett, J.W., Chu, W., Shaw, D., Kuglstatter, A.

(2010) Chem Biol Drug Des 76: 154-163

• PubMed: 20545945 
• DOI: 10.1111/j.1747-0285.2010.00993.x
• Primary Citation of Related Structures:  
  3MIY, 3MJ1, 3MJ2


• PubMed Abstract: 
  

IL-2-inducible T cell kinase plays an essential role in T cell receptor signaling and is considered a drug target for the treatment of Th2-mediated inflammatory diseases. By applying high-throughput protein engineering and crystallization, we have determined the X-ray crystal structures of IL-2-inducible T cell kinase in complex with its selective inhibitor BMS-509744 and the broad-spectrum kinase inhibitors sunitinib and RO5191614. Sunitinib uniquely stabilizes IL-2-inducible T cell kinase in the helix C-in conformation by inducing side chain conformational changes in the ATP-binding site. This preference of sunitinib to bind to an active kinase conformation is reflective of its broad-spectrum kinase activity. BMS-509744 uniquely stabilizes the activation loop in a substrate-blocking inactive conformation, indicating that structural changes described for Src family kinases are also involved in the regulation of IL-2-inducible T cell kinase activity. The observed BMS-509744 binding mode allows rationalization of structure-activity relationships reported for this inhibitor class and facilitates further structure-based drug design. Sequence-based analysis of this binding mode provides guidance for the rational design of inhibitor selectivity.

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Organizational Affiliation: 

Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ITK/TSK	A	266	Homo sapiens	Mutation(s): 3  Gene Names: ITK, EMT, LYK EC: 2.7.10.2
Find proteins for Q08881 (Homo sapiens) Explore Q08881  Go to UniProtKB:  Q08881
NIH Common Fund Data Resources
PHAROS:  Q08881 GTEx:  ENSG00000113263

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MJG	B [auth A]	N-[5-({5-[(4-acetylpiperazin-1-yl)carbonyl]-4-methoxy-2-methylphenyl}sulfanyl)-1,3-thiazol-2-yl]-4-({[(1S)-1,2,2-trimethylpropyl]amino}methyl)benzamide C32 H41 N5 O4 S2 ZHXNIYGJAOPMSO-NRFANRHFSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MJG	IC50:  15   nM  Binding MOAD
MJG	Ki:  16   nM  BindingDB
MJG	IC50 :  15   nM  PDBBind
MJG	IC50:  19   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.252 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.082	α = 90
b = 39.246	β = 93.69
c = 50.86	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-12 
• Released Date: 2010-06-30 
Deposition Author(s): Kuglstatter, A., Villasenor, A.G.

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance