3QGW

Crystal Structure of ITK kinase bound to an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery and structure-activity relationship of 3-aminopyrid-2-ones as potent and selective interleukin-2 inducible T-cell kinase (Itk) inhibitors

Charrier, J.D.Miller, A.Kay, D.P.Brenchley, G.Twin, H.C.Collier, P.N.Ramaya, S.Keily, S.B.Durrant, S.J.Knegtel, R.M.Tanner, A.J.Brown, K.Curnock, A.P.Jimenez, J.M.

(2011) J Med Chem 54: 2341-2350

  • DOI: 10.1021/jm101499u
  • Primary Citation of Related Structures:  
    3QGY, 3QGW

  • PubMed Abstract: 
  • Interleukin-2 inducible T-cell kinase (Itk) plays a role in T-cell functions, and its inhibition potentially represents an attractive intervention point to treat autoimmune and allergic diseases. Herein we describe the discovery of a series of potent and selective novel inhibitors of Itk ...

    Interleukin-2 inducible T-cell kinase (Itk) plays a role in T-cell functions, and its inhibition potentially represents an attractive intervention point to treat autoimmune and allergic diseases. Herein we describe the discovery of a series of potent and selective novel inhibitors of Itk. These inhibitors were identified by structure-based design, starting from a fragment generated de novo, the 3-aminopyrid-2-one motif. Functionalization of the 3-amino group enabled rapid enhancement of the inhibitory activity against Itk, while introduction of a substituted heteroaromatic ring in position 5 of the pyridone fragment was key to achieving optimal selectivity over related kinases. A careful analysis of the hydration patterns in the kinase active site was necessary to fully explain the observed selectivity profile. The best molecule prepared in this optimization campaign, 7v, inhibits Itk with a K(i) of 7 nM and has a good selectivity profile across kinases.


    Organizational Affiliation

    Department of Chemistry, Vertex Pharmaceuticals (Europe) Ltd., 88 Milton Park, Abingdon, Oxfordshire OX14 4RY, UK. jean-damien_charrier@vrtx.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSK AB286Homo sapiensMutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PQC
Query on PQC

Download Ideal Coordinates CCD File 
A
3-[(8-phenylthieno[2,3-h]quinazolin-2-yl)amino]benzenesulfonamide
C22 H16 N4 O2 S2
ZSSGEBJSMMYEMX-UHFFFAOYSA-N
 Ligand Interaction
L7A
Query on L7A

Download Ideal Coordinates CCD File 
B
N-(6-oxo-1,6-dihydro-3,4'-bipyridin-5-yl)benzamide
C17 H13 N3 O2
KASWEFFYPLWMCM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L7AKi:  1300   nM  Binding MOAD
L7AKi:  1300   nM  BindingDB
L7AKi :  1300   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.86α = 90
b = 74.38β = 94
c = 78.83γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance