Crystal structure of spleen tyrosine kinase complexed with an adamantylpyrazine inhibitor

Experimental Data Snapshot

  • Resolution: 2.48 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYK274Homo sapiensMutation(s): 0 
Gene Names: SYK
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens)
Explore P43405 
Go to UniProtKB:  P43405
PHAROS:  P43405
GTEx:  ENSG00000165025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43405
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0K1

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
0K1 Binding MOAD:  4DFN IC50: 20 (nM) from 1 assay(s)
PDBBind:  4DFN IC50: 20 (nM) from 1 assay(s)
BindingDB:  4DFN IC50: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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 = 40.295α = 90
b = 84.848β = 90
c = 90.996γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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