Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 32243.20 
• Atom Count: 2232 
• Residue Count: 274 
• 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


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.273 
• R-Value Work: 0.217 

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:  
  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.

---

Organizational Affiliation: 

Almirall-Barcelona Science Park Unit, Barcelona Science Park, 08028 Barcelona, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: SYK Go to UniProtKB:  P43405

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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 BINDINGMOAD
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 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 40.295	α = 90.00
b = 84.848	β = 90.00
c = 90.996	γ = 90.00

Software Package:

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

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
  Type: Advisory, Data collection
• Version 1.2: 2018-04-11
  Type: Data collection, Source and taxonomy