4YJO

THE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH GTC000222

• PDB DOI: https://doi.org/10.2210/pdb4YJO/pdb

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


• Deposited: 2015-03-03 Released: 2015-09-30 
• Deposition Author(s): Somers, D.O., Neu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: other

Literature

Discovery of GSK143, a highly potent, selective and orally efficacious spleen tyrosine kinase inhibitor.

Liddle, J., Atkinson, F.L., Barker, M.D., Carter, P.S., Curtis, N.R., Davis, R.P., Douault, C., Dickson, M.C., Elwes, D., Garton, N.S., Gray, M., Hayhow, T.G., Hobbs, C.I., Jones, E., Leach, S., Leavens, K., Lewis, H.D., McCleary, S., Neu, M., Patel, V.K., Preston, A.G., Ramirez-Molina, C., Shipley, T.J., Skone, P.A., Smithers, N., Somers, D.O., Walker, A.L., Watson, R.J., Weingarten, G.G.

(2011) Bioorg Med Chem Lett 21: 6188-6194

• PubMed: 21903390 
• DOI: https://doi.org/10.1016/j.bmcl.2011.07.082
• Primary Citation of Related Structures:  
  3SRV, 4YJO, 4YJP, 4YJQ, 4YJR, 4YJS, 4YJT, 4YJU


• PubMed Abstract: 
  

  The lead optimisation of the diaminopyrimidine carboxamide series of spleen tyrosine kinase inhibitors is described. The medicinal chemistry strategy was focused on optimising the human whole blood activity whilst achieving a sufficient margin over liability kinases and hERG activity. GSK143 is a potent and highly selective SYK inhibitor showing good efficacy in the rat Arthus model.

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Organizational Affiliation: 

GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK. [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: 33.2 kDa 
• Atom Count: 2,462 
• Modelled Residue Count: 267 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	281	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 GTEx:  ENSG00000165025

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4DF	B [auth A]	5-chloro-N~2~-(1,1-dioxido-2,3-dihydro-1,2-benzothiazol-6-yl)-N~4~-ethyl-N~4~-(1H-indazol-4-yl)pyrimidine-2,4-diamine C20 H18 Cl N7 O2 S XZUGISDIVDJNBC-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.936	α = 90
b = 84.821	β = 99.24
c = 40.412	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Somers, D.O., Neu, M.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description