3MJ2

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

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 

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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

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSKA266Homo sapiensMutation(s): 3 
Gene Names: ITK, EMT, LYK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q08881 (Homo sapiens)
Explore Q08881 
Go to UniProtKB:  Q08881
PHAROS:  Q08881
GTEx:  ENSG00000113263 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08881
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MJG
Query on MJG
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MJG BindingDB:  3MJ2 Ki: 16 (nM) from 1 assay(s)
IC50: 19 (nM) from 1 assay(s)
PDBBind:  3MJ2 IC50: 15 (nM) from 1 assay(s)
Binding MOAD:  3MJ2 IC50: 15 (nM) from 1 assay(s)
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 = 121.082α = 90
b = 39.246β = 93.69
c = 50.86γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2021-10-06
    Changes: Database references, Derived calculations