4FZ6

Crystal structure of spleen tyrosine kinase complexed with [6-((S)-2-Methyl-pyrrolidin-1-yl)-pyridin-2-yl]-(6-phenyl-imidazo[1,2-b]pyridazin-8-yl)-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Rational design of highly selective spleen tyrosine kinase inhibitors.

Lucas, M.C.Goldstein, D.M.Hermann, J.C.Kuglstatter, A.Liu, W.Luk, K.C.Padilla, F.Slade, M.Villasenor, A.G.Wanner, J.Xie, W.Zhang, X.Liao, C.

(2012) J.Med.Chem. 55: 10414-10423

  • DOI: 10.1021/jm301367c
  • Primary Citation of Related Structures:  4FYN, 4FYO

  • PubMed Abstract: 
  • A novel approach to design selective spleen tyrosine kinase (Syk) inhibitors is described. Inhibition of spleen tyrosine kinase has attracted much attention as a mechanism for the treatment of autoimmune diseases such as asthma, rheumatoid arthritis, ...

    A novel approach to design selective spleen tyrosine kinase (Syk) inhibitors is described. Inhibition of spleen tyrosine kinase has attracted much attention as a mechanism for the treatment of autoimmune diseases such as asthma, rheumatoid arthritis, and SLE. Fostamatinib, a Syk inhibitor that successfully completed phase II clinical trials, also exhibits some undesirable side effects. More selective Syk inhibitors could offer safer, alternative treatments. Through a systematic evaluation of the kinome, we identified Pro455 and Asn457 in the Syk ATP binding site as a rare combination among sequence aligned kinases and hypothesized that optimizing the interaction between them and a Syk inhibitor molecule would impart high selectivity for Syk over other kinases. We report the structure-guided identification of three series of selective spleen tyrosine kinase inhibitors that support our hypothesis and offer useful guidance to other researchers in the field.


    Organizational Affiliation

    Small Molecule Research, Discovery Chemistry, pRED, Pharma Research and Early Development, Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, New Jersey 07110, United States. matthew.lucas@cubist.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase SYK
A
291Homo sapiensGene 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
0VG
Query on 0VG

Download SDF File 
Download CCD File 
A
N-{6-[(2S)-2-methylpyrrolidin-1-yl]pyridin-2-yl}-6-phenylimidazo[1,2-b]pyridazin-8-amine
C22 H22 N6
OLNOLIZABHZSEW-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0VGIC50: 106.6 nM (100) BINDINGDB
0VGIC50: 127 nM BINDINGMOAD
0VGIC50: 127 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.764α = 90.00
b = 85.072β = 90.00
c = 90.464γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release