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 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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:  
    4FYO, 4FZ6, 4FYN

  • 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, and SLE ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYKA291Homo sapiensMutation(s): 0 
Gene Names: SYK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0VG (Subject of Investigation/LOI)
Query on 0VG

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
0VG BindingDB:  4FZ6 IC50: min: 106.6, max: 127.3 (nM) from 3 assay(s)
Binding MOAD:  4FZ6 IC50: 127 (nM) from 1 assay(s)
PDBBind:  4FZ6 IC50: 127 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.764α = 90
b = 85.072β = 90
c = 90.464γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description