4RFM

ITK kinase domain in complex with compound 1 N-{1-[(1,1-dioxo-1-thian-2-yl)(phenyl)methyl]-1H- pyrazol-4-yl}-5,5-difluoro-5a-methyl-1H,4H,4aH,5H,5aH,6H-cyclopropa[f]indazole-3-carboxamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Tetrahydroindazoles as Interleukin-2 Inducible T-Cell Kinase Inhibitors. Part II. Second-Generation Analogues with Enhanced Potency, Selectivity, and Pharmacodynamic Modulation in Vivo.

Burch, J.D., Barrett, K., Chen, Y., DeVoss, J., Eigenbrot, C., Goldsmith, R., Ismaili, M.H., Lau, K., Lin, Z., Ortwine, D.F., Zarrin, A.A., McEwan, P.A., Barker, J.J., Ellebrandt, C., Kordt, D., Stein, D.B., Wang, X., Chen, Y., Hu, B., Xu, X., Yuen, P.W., Zhang, Y., Pei, Z.

(2015) J.Med.Chem. 58: 3806-3816

  • DOI: 10.1021/jm501998m

  • PubMed Abstract: 

    • The medicinal chemistry community has directed considerable efforts toward the discovery of selective inhibitors of interleukin-2 inducible T-cell kinase (ITK), given its role in T-cell signaling downstream of the T-cell receptor (TCR) and the implic ...

    The medicinal chemistry community has directed considerable efforts toward the discovery of selective inhibitors of interleukin-2 inducible T-cell kinase (ITK), given its role in T-cell signaling downstream of the T-cell receptor (TCR) and the implications of this target for inflammatory disorders such as asthma. We have previously disclosed a structure- and property-guided lead optimization effort which resulted in the discovery of a new series of tetrahydroindazole-containing selective ITK inhibitors. Herein we disclose further optimization of this series that resulted in further potency improvements, reduced off-target receptor binding liabilities, and reduced cytotoxicity. Specifically, we have identified a correlation between the basicity of solubilizing elements in the ITK inhibitors and off-target antiproliferative effects, which was exploited to reduce cytotoxicity while maintaining kinase selectivity. Optimized analogues were shown to reduce IL-2 and IL-13 production in vivo following oral or intraperitoneal dosing in mice.

    Organizational Affiliation: 

    ∥Pharmaron Beijing Ltd. Co., No. 6 TaiHe Road BDA, 100176 Beijing, P. R. China.,†Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States.,‡Evotec (U.K.) Ltd., 114 Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom.,§Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ITK/TSK
A
266Homo sapiensMutation(s): 3 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3P6
Query on 3P6
Download SDF File 
Download CCD File 
A
(4aS,5aR)-N-{1-[(R)-[(2R)-1,1-dioxidotetrahydro-2H-thiopyran-2-yl](phenyl)methyl]-1H-pyrazol-4-yl}-5,5-difluoro-5a-methyl-1,4,4a,5,5a,6-hexahydrocyclopropa[f]indazole-3-carboxamide
C25 H27 F2 N5 O3 S
JNRFIKALOWSUBG-DAVFGYKESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3P6Ki: 0.1 nM (98) BINDINGDB
3P6IC50: 4 nM (98) BINDINGDB
3P6Ki: 0.09 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.006α = 90.00
b = 69.561β = 113.39
c = 47.347γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
d*TREKdata reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-08-26
    Type: Database references