4FYN

Crystal structure of spleen tyrosine kinase complexed with 3-(8-{4-[Ethyl-(2-hydroxy-ethyl)-amino]-phenylamino}-imidazo[1,2-a]pyrazin-5-yl)-phenol

• PDB DOI:  https://doi.org/10.2210/pdb4FYN/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-07-05 Released: 2013-01-30 
• Deposition Author(s): Kuglstatter, A., Villasenor, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.269 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

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

• PubMed: 23151054 
• DOI: https://doi.org/10.1021/jm301367c
• Primary Citation of Related Structures:  
  4FYN, 4FYO, 4FZ6


• 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. 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.

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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. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 34.27 kDa 
• Atom Count: 2,254 
• Modelled Residue Count: 267 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	291	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0VE	B [auth A]	3-[8-({4-[ethyl(2-hydroxyethyl)amino]phenyl}amino)imidazo[1,2-a]pyrazin-5-yl]phenol C22 H23 N5 O2 HNXXZSFGRGLZTI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.269 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.958	α = 90
b = 85.112	β = 90
c = 90.752	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Kuglstatter, A., Villasenor, A.G.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description