4F4P | pdb_00004f4p

SYK in COMPLEX WITH LIGAND LASW836

• PDB DOI: https://doi.org/10.2210/pdb4F4P/pdb

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


• Deposited: 2012-05-11 Released: 2012-12-12 
• Deposition Author(s): Lopez, M., Segarra, V., Vidal, B., Wenzkowski, C., Jestel, A., Krapp, S., Blaesse, M., Nagel, S., Schreiner, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.285 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Highly potent aminopyridines as Syk kinase inhibitors.

Castillo, M., Forns, P., Erra, M., Mir, M., Lopez, M., Maldonado, M., Orellana, A., Carreno, C., Ramis, I., Miralpeix, M., Vidal, B.

(2012) Bioorg Med Chem Lett 22: 5419-5423

• PubMed: 22877633 
• DOI: https://doi.org/10.1016/j.bmcl.2012.07.045
• Primary Citation Related Structures: 
  4F4P


• PubMed Abstract: 
  

  A novel class of potent Syk inhibitors has been developed from rational design. Highly potent aminopyridine derivatives bearing a 4-trifluoromethyl-2-pyridyl motif and represented by compound 13b IC(50): 0.6 nM were identified. Substitution by a 2-pyrazinyl motif and SAR expansion in position 4 of the central core provided diverse potent non-cytotoxic Syk inhibitors showing nanomolar activity inhibiting human mast cell line LAD2 degranulation.

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Organizational Affiliation: 
• Almirall-Barcelona Science Park Unit, Barcelona Science Park, 08028 Barcelona, Spain.

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: 32.09 kDa 
• Atom Count: 2,197 
• Modeled Residue Count: 262 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	273	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
0SB	B [auth A]	N-{6-[3-(piperazin-1-yl)phenyl]pyridin-2-yl}-4-(trifluoromethyl)pyridin-2-amine C21 H20 F3 N5 FCPDILGNMHIWJE-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.285 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.501	α = 90
b = 84.227	β = 90
c = 89.819	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Lopez, M., Segarra, V., Vidal, B., Wenzkowski, C., Jestel, A., Krapp, S., Blaesse, M., Nagel, S., Schreiner, P.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Advisory, Structure summary
• Version 1.2: 2024-02-28
  Changes: Advisory, Data collection, Database references, Derived calculations