X-ray crystal structure of ITK complexed with sunitinib

Experimental Data Snapshot

  • Resolution: 1.67 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

Starting Model: experimental
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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: https://doi.org/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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSK
A, B
266Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for Q08881 (Homo sapiens)
Explore Q08881 
Go to UniProtKB:  Q08881
GTEx:  ENSG00000113263 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08881
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B49

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide
C22 H27 F N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
B49 PDBBind:  3MIY Kd: 21 (nM) from 1 assay(s)
BindingDB:  3MIY Kd: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.67 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.479α = 98.49
b = 52.053β = 103.65
c = 66.106γ = 92.84
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

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: Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Atomic model
  • Version 1.3: 2021-10-06
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description