ITK kinase domain with compound GNE-9822

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Property- and structure-guided discovery of a tetrahydroindazole series of interleukin-2 inducible T-cell kinase inhibitors.

Burch, J.D.Lau, K.Barker, J.J.Brookfield, F.Chen, Y.Chen, Y.Eigenbrot, C.Ellebrandt, C.Ismaili, M.H.Johnson, A.Kordt, D.MacKinnon, C.H.McEwan, P.A.Ortwine, D.F.Stein, D.B.Wang, X.Winkler, D.Yuen, P.W.Zhang, Y.Zarrin, A.A.Pei, Z.

(2014) J Med Chem 57: 5714-5727

  • DOI: https://doi.org/10.1021/jm500550e
  • Primary Citation of Related Structures:  
    4PQN, 4PRJ

  • PubMed Abstract: 

    Interleukin-2 inducible T-cell kinase (ITK), a member of the Tec family of tyrosine kinases, plays a major role in T-cell signaling downstream of the T-cell receptor (TCR), and considerable efforts have been directed toward discovery of ITK-selective inhibitors as potential treatments of inflammatory disorders such as asthma. Using a previously disclosed indazole series of inhibitors as a starting point, and using X-ray crystallography and solubility forecast index (SFI) as guides, we evolved a series of tetrahydroindazole inhibitors with improved potency, selectivity, and pharmaceutical properties. Highlights include identification of a selectivity pocket above the ligand plane, and identification of appropriate lipophilic substituents to occupy this space. This effort culminated in identification of a potent and selective ITK inhibitor (GNE-9822) with good ADME properties in preclinical species.

  • Organizational Affiliation

    Genentech Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ITK/TSK266Homo sapiensMutation(s): 3 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2W6

Download Ideal Coordinates CCD File 
B [auth A]N-{1-[(1S)-3-(dimethylamino)-1-phenylpropyl]-1H-pyrazol-4-yl}-6,6-dimethyl-4,5,6,7-tetrahydro-1H-indazole-3-carboxamide
C24 H32 N6 O
Query on P4G

Download Ideal Coordinates CCD File 
C8 H18 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
2W6 BindingDB:  4PQN Ki: 0.7 (nM) from 1 assay(s)
IC50: min: 45, max: 55 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.71 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.18α = 90
b = 39.03β = 93.07
c = 50.68γ = 90
Software Package:
Software NamePurpose
GDAdata collection
XDSdata reduction
SCALAdata 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: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description