4L7S | pdb_00004l7s

Kinase domain mutant of human Itk in complex with an aminobenzothiazole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.221 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4L7S

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Identification of a Novel and Selective Series of Itk Inhibitors via a Template-Hopping Strategy.

Alder, C.M.Ambler, M.Campbell, A.J.Champigny, A.C.Deakin, A.M.Harling, J.D.Harris, C.A.Longstaff, T.Lynn, S.Maxwell, A.C.Mooney, C.J.Scullion, C.Singh, O.M.Smith, I.E.Somers, D.O.Tame, C.J.Wayne, G.Wilson, C.Woolven, J.M.

(2013) ACS Med Chem Lett 4: 948-952

  • DOI: https://doi.org/10.1021/ml400206q
  • Primary Citation Related Structures: 
    4L7S

  • PubMed Abstract: 

    Inhibition of Itk potentially constitutes a novel, nonsteroidal treatment for asthma and other T-cell mediated diseases. In-house kinase cross-screening resulted in the identification of an aminopyrazole-based series of Itk inhibitors. Initial work on this series highlighted selectivity issues with several other kinases, particularly AurA and AurB. A template-hopping strategy was used to identify a series of aminobenzothiazole Itk inhibitors, which utilized an inherently more selective hinge binding motif. Crystallography and modeling were used to rationalize the observed selectivity. Initial exploration of the SAR around this series identified potent Itk inhibitors in both enzyme and cellular assays.


  • Organizational Affiliation
    • Respiratory Therapy Area Unit, GlaxoSmithKline Pharmaceuticals , Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, U.K.

Macromolecule Content 

  • Total Structure Weight: 61.56 kDa 
  • Atom Count: 4,439 
  • Modeled Residue Count: 500 
  • Deposited Residue Count: 532 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSK
A, B
266Homo sapiensMutation(s): 1 
Gene Names: ITKEMTLYK
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G7K

Query on G7K



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
trans-4-({4-[difluoro(4-fluorophenyl)methyl]-6-[(5-methoxy[1,3]thiazolo[5,4-b]pyridin-2-yl)amino]pyrimidin-2-yl}amino)cyclohexanol
C24 H23 F3 N6 O2 S
PFDUFECOJKSDAT-WKILWMFISA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.221 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.857α = 90
b = 69.523β = 108.18
c = 68.617γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-01-22 
  • Deposition Author(s): Somers, D.O.

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations