4RX9 | pdb_00004rx9

SYK Catalytic Domain Complexed with a Potent Pyrimidine Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4RX9/pdb

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


• Deposited: 2014-12-09 Released: 2015-03-18 
• Deposition Author(s): Lee, C.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Discovery and profiling of a selective and efficacious syk inhibitor.

Thoma, G., Smith, A.B., van Eis, M.J., Vangrevelinghe, E., Blanz, J., Aichholz, R., Littlewood-Evans, A., Lee, C.C., Liu, H., Zerwes, H.G.

(2015) J Med Chem 58: 1950-1963

• PubMed: 25633741 
• DOI: https://doi.org/10.1021/jm5018863
• Primary Citation Related Structures: 
  4RX7, 4RX8, 4RX9


• PubMed Abstract: 
  

  We describe the discovery of selective and potent Syk inhibitor 11, which exhibited favorable PK profiles in rat and dog and was found to be active in a collagen-induced arthritis model in rats. Compound 11 was selected for further profiling, but, unfortunately, in GLP toxicological studies it showed liver findings in rat and dog. Nevertheless, 11 could become a valuable tool compound to investigate the rich biology of Syk in vitro and in vivo.

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Organizational Affiliation: 
• Global Discovery Chemistry, ‡Analytical Sciences & Imaging, §Autoimmunity, Transplantation and Inflammation Research, Novartis Institutes for Biomedical Research , 4056 Basel, Switzerland.

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: 34.29 kDa 
• Atom Count: 2,416 
• Modeled Residue Count: 268 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	290	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
3YT	C [auth A]	2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-{[3-(2H-1,2,3-triazol-2-yl)phenyl]amino}pyrimidine-5-carboxamide C19 H23 N9 O TXGKRVFSSHPBAJ-JKSUJKDBSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3YT	BindingDB:  4RX9	IC50: min: 1, max: 1.00e+4 (nM) from 15 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.197 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.978	α = 90
b = 85.126	β = 90
c = 89.776	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Lee, C.C.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations