4HCT

Crystal structure of ITK in complex with compound 52

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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Literature

Covalent inhibitors of interleukin-2 inducible T cell kinase (itk) with nanomolar potency in a whole-blood assay.

Zapf, C.W., Gerstenberger, B.S., Xing, L., Limburg, D.C., Anderson, D.R., Caspers, N., Han, S., Aulabaugh, A., Kurumbail, R., Shakya, S., Li, X., Spaulding, V., Czerwinski, R.M., Seth, N., Medley, Q.G.

(2012) J Med Chem 55: 10047-10063

  • DOI: 10.1021/jm301190s
  • Primary Citation of Related Structures:  
    4HCT, 4HCU, 4HCV

  • PubMed Abstract: 

    • We wish to report a strategy that targets interleukin-2 inducible T cell kinase (Itk) with covalent inhibitors. Thus far, covalent inhibition of Itk has not been disclosed in the literature. Structure-based drug design was utilized to achieve low nanomolar potency of the disclosed series even at high ATP concentrations ...

    We wish to report a strategy that targets interleukin-2 inducible T cell kinase (Itk) with covalent inhibitors. Thus far, covalent inhibition of Itk has not been disclosed in the literature. Structure-based drug design was utilized to achieve low nanomolar potency of the disclosed series even at high ATP concentrations. Kinetic measurements confirmed an irreversible binding mode with off-rate half-lives exceeding 24 h and moderate on-rates. The analogues are highly potent in a cellular IP1 assay as well as in a human whole-blood (hWB) assay. Despite a half-life of approximately 2 h in resting primary T cells, the covalent inhibition of Itk resulted in functional silencing of the TCR pathway for more than 24 h. This prolonged effect indicates that covalent inhibition is a viable strategy to target the inactivation of Itk.

    Organizational Affiliation: 

    BioTherapeutics Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, USA. christoph.zapf@pfizer.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSKA269Homo sapiensMutation(s): 1 
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
18R
Query on 18R
Download Ideal Coordinates CCD File 
B [auth A]3-{1-[(3R)-1-acryloylpiperidin-3-yl]-4-amino-1H-pyrazolo[3,4-d]pyrimidin-3-yl}-N-(3-tert-butylphenyl)benzamide
C30 H33 N7 O2
RMAUIYTVKFMOGP-HSZRJFAPSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
18R PDBBind:  4HCT IC50: 73 (nM) from 1 assay(s)
BindingDB:  4HCT IC50: min: 10, max: 2210 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.41α = 90
b = 67.85β = 111.23
c = 49.28γ = 90
Software Package:
Software NamePurpose
AutoPROCdata collection
BUSTERrefinement
AutoPROCdata scaling
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references