4HCU

Crystal structure of ITK in complext with compound 40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • 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 nan ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ITK/TSK
A
269Homo sapiensMutations: R245K
Gene Names: ITK (EMT, LYK)
EC: 2.7.10.2
Find proteins for Q08881 (Homo sapiens)
Go to Gene View: ITK
Go to UniProtKB:  Q08881
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13L
Query on 13L

Download SDF File 
Download CCD File 
A
3-{4-amino-1-[(3R)-1-propanoylpiperidin-3-yl]-1H-pyrazolo[3,4-d]pyrimidin-3-yl}-N-[4-(propan-2-yl)phenyl]benzamide
C29 H33 N7 O2
OQUNLLPGZMGVNR-HSZRJFAPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
13LIC50: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.530α = 90.00
b = 68.050β = 111.42
c = 49.230γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
AutoPROCdata collection
PHASERphasing
AutoPROCdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-01 
  • Released Date: 2012-11-14 
  • Deposition Author(s): Han, S., Caspers, N.

Revision History 

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