4DFN

Crystal structure of spleen tyrosine kinase complexed with an adamantylpyrazine inhibitor


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYKA274Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0K1 (Subject of Investigation/LOI)
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
KADWYJUBGMHRCN-QWOVOEGBSA-N
 Ligand Interaction
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

  • 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 = 40.295α = 90
b = 84.848β = 90
c = 90.996γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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