3TUD

Crystal structure of SYK kinase domain with N-(4-methyl-3-(8-methyl-7-oxo-2-(phenylamino)-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl)phenyl)-3-(trifluoromethyl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1111/j.1747-0285.2012.01443.x
  • Primary Citation of Related Structures:  

  • 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 des ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase SYK
A
299Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
Find proteins for P43405 (Homo sapiens)
Go to Gene View: SYK
Go to UniProtKB:  P43405
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FPX
Query on FPX

Download SDF File 
Download CCD File 
A
N-{4-methyl-3-[8-methyl-7-oxo-2-(phenylamino)-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl]phenyl}-3-(trifluoromethyl)benzamide
C29 H22 F3 N5 O2
IMLLFFIWQIAPHC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FPXIC50: 2.1 nM (100) BINDINGDB
FPXIC50: 2.1 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.799α = 90.00
b = 68.066β = 90.00
c = 82.790γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data collection
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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