4DFL

Crystal structure of spleen tyrosine kinase complexed with a sulfonamidopyrazine piperidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4DFL/pdb

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


• Deposited: 2012-01-24 Released: 2012-04-25 
• 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: 1.98 Å
• R-Value Free: 0.243 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Literature

Pyrazine-based Syk kinase inhibitors.

Forns, P., Esteve, C., Taboada, L., Alonso, J.A., Orellana, A., Maldonado, M., Carreno, C., Ramis, I., Lopez, M., Miralpeix, M., Vidal, B.

(2012) Bioorg Med Chem Lett 22: 2784-2788

• PubMed: 22425453 
• DOI: https://doi.org/10.1016/j.bmcl.2012.02.087
• Primary Citation of Related Structures:  
  4DFL, 4DFN


• PubMed Abstract: 
  

  A series of aminopyrazines as inhibitors of Syk kinase activity and showing inhibition of LAD2 cells degranulation is described. Optimization of the carboxamide motif with aminomethylpiperidines provided high potency inhibiting Syk but low cellular activity. Amides of cis and trans adamantanol showed good inhibitory activity against Syk as well as remarkable activity in LAD2 cells degranulation assay.

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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: 32.36 kDa 
• Atom Count: 2,291 
• Modelled Residue Count: 263 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	274	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) Go to UniProtKB:  P43405
PHAROS:  P43405 GTEx:  ENSG00000165025

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0K0	B [auth A]	3-amino-6-{3-[(methylsulfonyl)amino]phenyl}-N-(piperidin-4-ylmethyl)pyrazine-2-carboxamide C18 H24 N6 O3 S UCJDFWBCXROCMH-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0K0	PDBBind:  4DFL	IC50: 670 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.243 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.028	α = 90
b = 85.004	β = 90
c = 90.748	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: 2012-04-25 
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: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2018-04-11
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-02-28
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary