4YJR | pdb_00004yjr

SYK kinase domain in complex with inhibitor GTC000225

• PDB DOI: https://doi.org/10.2210/pdb4YJR/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., Stuckey, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.180 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

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 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: 33.23 kDa 
• Atom Count: 2,592 
• Modeled Residue Count: 265 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4DJ	B [auth A]	3-(1H-indazol-4-yl{2-[(1-methyl-1H-indazol-5-yl)amino]pyrimidin-4-yl}amino)propan-1-ol C22 H22 N8 O VKBDFJNINXDOJC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
4DJ	BindingDB:  4YJR	IC50: min: 18.5, max: 20.6 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.180 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.43	α = 90
b = 86.63	β = 93.49
c = 40.27	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary