ITK kinase domain with compound 28 (N-{1-[(1S)-3-(DIMETHYLAMINO)-1-PHENYLPROPYL]-1H-PYRAZOL-4-YL}-6-(1H-PYRAZOL-4-YL)-1H-INDAZOLE-3-CARBOXAMIDE)

Experimental Data Snapshot

  • Resolution: 2.82 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

Starting Model: experimental
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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery and optimization of indazoles as potent and selective interleukin-2 inducible T cell kinase (ITK) inhibitors.

Pastor, R.M.Burch, J.D.Magnuson, S.Ortwine, D.F.Chen, Y.De La Torre, K.Ding, X.Eigenbrot, C.Johnson, A.Liimatta, M.Liu, Y.Shia, S.Wang, X.Wu, L.C.Pei, Z.

(2014) Bioorg Med Chem Lett 24: 2448-2452

  • DOI: https://doi.org/10.1016/j.bmcl.2014.04.023
  • Primary Citation of Related Structures:  
    4PP9, 4PPA, 4PPB, 4PPC

  • PubMed Abstract: 

    There is evidence that small molecule inhibitors of the non-receptor tyrosine kinase ITK, a component of the T-cell receptor signaling cascade, could represent a novel asthma therapeutic class. Moreover, given the expected chronic dosing regimen of any asthma treatment, highly selective as well as potent inhibitors would be strongly preferred in any potential therapeutic. Here we report hit-to-lead optimization of a series of indazoles that demonstrate sub-nanomolar inhibitory potency against ITK with strong cellular activity and good kinase selectivity. We also elucidate the binding mode of these inhibitors by solving the X-ray crystal structures of the complexes.

  • Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: pastor.richard@gene.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSK
A, B
266Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q08881 (Homo sapiens)
Explore Q08881 
Go to UniProtKB:  Q08881
GTEx:  ENSG00000113263 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08881
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2VV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C25 H26 N8 O
Binding Affinity Annotations 
IDSourceBinding Affinity
2VV BindingDB:  4PPB Ki: 0.1 (nM) from 1 assay(s)
IC50: min: 25, max: 173 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.82 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.937α = 90
b = 94.407β = 90
c = 156.206γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Experimental preparation
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description