Crystal structure of SYK kinase domain with 1-(5-(6,7-dimethoxyquinolin-4-yloxy)pyridin-2-yl)-3-((1R,2S)-2-phenylcyclopropyl)urea

Experimental Data Snapshot

  • Resolution: 2.23 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Identification of Type-II Inhibitors Using Kinase Structures.

Lovering, F.McDonald, J.Whitlock, G.A.Glossop, P.A.Phillips, C.Bent, A.Sabnis, Y.Ryan, M.Fitz, L.Lee, J.Chang, J.S.Han, S.Kurumbail, R.Thorarensen, A.

(2012) Chem Biol Drug Des 80: 657-664

  • DOI: https://doi.org/10.1111/j.1747-0285.2012.01443.x
  • Primary Citation of Related Structures:  
    3TUB, 3TUC, 3TUD

  • PubMed Abstract: 

    Spleen tyrosine kinase is a non-receptor tyrosine kinase, overactivation of which is thought to contribute to autoimmune diseases as well as allergy and asthma. Protein kinases have a highly conserved ATP binding site, thus making challenging the design of selective small molecule inhibitors. It has been well documented that some protein kinases can be stabilized in their inactive conformations (Type-II inhibitors). Herein, we describe a protein structure/ligand-based approach to successfully identify ligands that bind to novel conformations of spleen tyrosine kinase. By utilizing kinase protein crystal structures both in the public domain (RCSB) and within Pfizer's protein crystal database, we report the discovery of the first spleen tyrosine kinase Type-II ligands. Compounds 1 and 3 were found to bind to the DFG-out conformation of spleen tyrosine kinase, while compound 2 binds to a DFG-in, C-Helix-out conformation. In this instance, the C-helix moved significantly to create a large hydrophobic pocket rarely seen in kinase protein crystal structures.

  • Organizational Affiliation

    World Wide Medicinal Chemistry, Pfizer Worldwide R & D, 200 Cambridgepark Drive, Cambridge, MA 02140, USA. frank.lovering@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK293Homo sapiensMutation(s): 0 
Gene Names: SYK
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
GTEx:  ENSG00000165025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43405
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FPU

Download Ideal Coordinates CCD File 
B [auth A]1-{5-[(6,7-dimethoxyquinolin-4-yl)oxy]pyridin-2-yl}-3-[(1R,2S)-2-phenylcyclopropyl]urea
C26 H24 N4 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
FPU Binding MOAD:  3TUB IC50: 320 (nM) from 1 assay(s)
BindingDB:  3TUB IC50: 320 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.23 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.92α = 90
b = 71.62β = 90
c = 84.21γ = 90
Software Package:
Software NamePurpose
AutoPROCdata collection
AutoPROCdata scaling
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2012-08-29 
  • Deposition Author(s): Han, S.

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references