3QGY

Crystal structure of ITK inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 

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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ITK/TSK
A, B
286Homo sapiensMutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L7O
Query on L7O

Download SDF File 
Download CCD File 
B
N-{5-[2-(methylamino)pyrimidin-4-yl]-2-oxo-1,2-dihydropyridin-3-yl}-4-(piperidin-1-yl)benzamide
3-(4-(Piperidin-1-yl)benzoylamino)-5-(2-(methylamino)pyrimidin-4-yl)-(1H)-pyridin-2-one
C22 H24 N6 O2
MKSQDWBNZVGINB-UHFFFAOYSA-N
 Ligand Interaction
PQC
Query on PQC

Download SDF File 
Download CCD File 
A
3-[(8-phenylthieno[2,3-h]quinazolin-2-yl)amino]benzenesulfonamide
C22 H16 N4 O2 S2
ZSSGEBJSMMYEMX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L7OKi: 16 nM (89) BINDINGDB
L7OKi: 16 nM BINDINGMOAD
L7OKi: 16 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.860α = 90.00
b = 74.381β = 93.99
c = 78.833γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
SCALAdata scaling
CNSrefinement
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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