4KIO

Kinase domain mutant of human Itk in complex with a covalently-binding inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of novel irreversible inhibitors of interleukin (IL)-2-inducible tyrosine kinase (Itk) by targeting cysteine 442 in the ATP pocket.

Harling, J.D.Deakin, A.M.Campos, S.Grimley, R.Chaudry, L.Nye, C.Polyakova, O.Bessant, C.M.Barton, N.Somers, D.Barrett, J.Graves, R.H.Hanns, L.Kerr, W.J.Solari, R.

(2013) J Biol Chem 288: 28195-28206

  • DOI: 10.1074/jbc.M113.474114
  • Primary Citation of Related Structures:  
    4KIO

  • PubMed Abstract: 
  • IL-2-inducible tyrosine kinase (Itk) plays a key role in antigen receptor signaling in T cells and is considered an important target for anti-inflammatory drug discovery. In order to generate inhibitors with the necessary potency and selectivity, a compound that targeted cysteine 442 in the ATP binding pocket and with an envisaged irreversible mode of action was designed ...

    IL-2-inducible tyrosine kinase (Itk) plays a key role in antigen receptor signaling in T cells and is considered an important target for anti-inflammatory drug discovery. In order to generate inhibitors with the necessary potency and selectivity, a compound that targeted cysteine 442 in the ATP binding pocket and with an envisaged irreversible mode of action was designed. We incorporated a high degree of molecular recognition and specific design features making the compound suitable for inhaled delivery. This study confirms the irreversible covalent binding of the inhibitor to the kinase by x-ray crystallography and enzymology while demonstrating potency, selectivity, and prolonged duration of action in in vitro biological assays. The biosynthetic turnover of the kinase was also examined as a critical factor when designing irreversible inhibitors for extended duration of action. The exemplified Itk inhibitor demonstrated inhibition of both TH1 and TH2 cytokines, was additive with fluticasone propionate, and inhibited cytokine release from human lung fragments. Finally, we describe an in vivo pharmacodynamic assay that allows rapid preclinical development without animal efficacy models.


    Organizational Affiliation

    From the Allergic Inflammation Discovery Performance Unit and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSK ABCD266Homo sapiensMutation(s): 1 
Gene Names: ITKEMTLYK
EC: 2.7.10.2
Find proteins for Q08881 (Homo sapiens)
Explore Q08881 
Go to UniProtKB:  Q08881
NIH Common Fund Data Resources
PHAROS:  Q08881
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6K
Query on G6K

Download Ideal Coordinates CCD File 
C, D
1-[(3S)-3-{[4-(morpholin-4-ylmethyl)-6-([1,3]thiazolo[5,4-b]pyridin-2-ylamino)pyrimidin-2-yl]amino}pyrrolidin-1-yl]propan-1-one
C22 H28 N8 O2 S
JSHRNKDQLCOTRI-HNNXBMFYSA-N
 Ligand Interaction
G5K
Query on G5K

Download Ideal Coordinates CCD File 
A, B, C
1-[(3S)-3-{[4-(morpholin-4-ylmethyl)-6-([1,3]thiazolo[5,4-b]pyridin-2-ylamino)pyrimidin-2-yl]amino}pyrrolidin-1-yl]prop-2-en-1-one
C22 H26 N8 O2 S
LZANMDGKZJPQIB-HNNXBMFYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G5KIC50 :  501   nM  PDBBind
G5KIC50:  500   nM  BindingDB
G5KIC50:  500   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.309α = 90
b = 69.279β = 100.87
c = 141.852γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-05-02 
  • Released Date: 2013-08-21 
  • Deposition Author(s): Somers, D.O.

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references