4QD6 | pdb_00004qd6

ITK kinase domain in complex with inhibitor compound

• PDB DOI: https://doi.org/10.2210/pdb4QD6/pdb

• Classification: Transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-05-13 Released: 2015-01-14 
• Deposition Author(s): McEwan, P.A., Barker, J.J., Eigenbrot, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.267 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Design, synthesis and structure-activity relationships of a novel class of sulfonylpyridine inhibitors of Interleukin-2 inducible T-cell kinase (ITK).

Trani, G., Barker, J.J., Bromidge, S.M., Brookfield, F.A., Burch, J.D., Chen, Y., Eigenbrot, C., Heifetz, A., Ismaili, M.H., Johnson, A., Krulle, T.M., MacKinnon, C.H., Maghames, R., McEwan, P.A., Montalbetti, C.A., Ortwine, D.F., Perez-Fuertes, Y., Vaidya, D.G., Wang, X., Zarrin, A.A., Pei, Z.

(2014) Bioorg Med Chem Lett 24: 5818-5823

• PubMed: 25455497 
• DOI: https://doi.org/10.1016/j.bmcl.2014.10.020
• Primary Citation Related Structures: 
  4QD6


• PubMed Abstract: 
  

  Starting from benzylpyrimidine 2, molecular modeling and X-ray crystallography were used to design highly potent inhibitors of Interleukin-2 inducible T-cell kinase (ITK). Sulfonylpyridine 4i showed sub-nanomolar affinity against ITK, was selective versus Lck and its activity in the Jurkat cell-based assay was greatly improved over 2.

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Organizational Affiliation: 
• Discovery Chemistry, Evotec UK Ltd, 114 Innovation Drive, Milton Park, Abingdon, OX14 4RZ, UK. Electronic address: [e-mail].
Discovery Chemistry, Evotec UK Ltd, 114 Innovation Drive, Milton Park, Abingdon, OX14 4RZ, UK.
Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
Discovery Biology, Evotec AG, Manfred Eigen Campus, Essener Bogen 7, D-22419 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.41 kDa 
• Atom Count: 3,988 
• Modeled Residue Count: 487 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ITK/TSK	A, B	266	Homo sapiens	Mutation(s): 1  Gene Names: ITK, EMT, LYK 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
30T	C [auth A], D [auth B]	trans-4-({6-[(5-phenyl-1H-pyrazol-3-yl)amino]-4-(phenylsulfonyl)pyridin-2-yl}amino)cyclohexanol C26 H27 N5 O3 S YIGXUZJWVOKKIO-MXVIHJGJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.267 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.06	α = 90
b = 94.32	β = 90
c = 156.34	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): McEwan, P.A., Barker, J.J., Eigenbrot, C.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations