Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.24 kDa 
• Atom Count: 2254 
• Residue Count: 269 
• Unique protein chains: 1

4DFN

Crystal structure of spleen tyrosine kinase complexed with an adamantylpyrazine inhibitor

• DOI: 10.2210/pdb4DFN/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: 2.48 Å
• R-Value Free: 0.273 
• R-Value Work: 0.217 
• R-Value Observed: 0.222 

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: 10.1016/j.bmcl.2012.02.087
• Primary Citation of Related Structures:  
  4DFN, 4DFL


• 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.

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
Find proteins for P43405 (Homo sapiens) Explore P43405  Go to UniProtKB:  P43405
NIH Common Fund Data Resources
PHAROS  P43405 GTEx  ENSG00000165025

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0K1	A	3-amino-6-[3-(1-methyl-1H-pyrazol-4-yl)phenyl]-N-[(1R,2r,3S,5s,7s)-5-hydroxyadamantan-2-yl]pyrazine-2-carboxamide C25 H28 N6 O2 KADWYJUBGMHRCN-QWOVOEGBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0K1	IC50:  40   nM  Binding MOAD
0K1	IC50 :  20   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.273 
• R-Value Work: 0.217 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.295	α = 90
b = 84.848	β = 90
c = 90.996	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

• Deposited Date: 2012-01-24 
• 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: 2018-04-04
  Changes: Advisory, Data collection
• Version 1.2: 2018-04-11
  Changes: Data collection, Source and taxonomy