4FIC

Kinase domain of cSrc in complex with a hinge region-binding fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

De novo design of protein kinase inhibitors by in silico identification of hinge region-binding fragments.

Urich, R.Wishart, G.Kiczun, M.Richters, A.Tidten-Luksch, N.Rauh, D.Sherborne, B.Wyatt, P.G.Brenk, R.

(2013) Acs Chem.Biol. 8: 1044-1052

  • DOI: 10.1021/cb300729y

  • PubMed Abstract: 
  • Protein kinases constitute an attractive family of enzyme targets with high relevance to cell and disease biology. Small molecule inhibitors are powerful tools to dissect and elucidate the function of kinases in chemical biology research and to serve ...

    Protein kinases constitute an attractive family of enzyme targets with high relevance to cell and disease biology. Small molecule inhibitors are powerful tools to dissect and elucidate the function of kinases in chemical biology research and to serve as potential starting points for drug discovery. However, the discovery and development of novel inhibitors remains challenging. Here, we describe a structure-based de novo design approach that generates novel, hinge-binding fragments that are synthetically feasible and can be elaborated to small molecule libraries. Starting from commercially available compounds, core fragments were extracted, filtered for pharmacophoric properties compatible with hinge-region binding, and docked into a panel of protein kinases. Fragments with a high consensus score were subsequently short-listed for synthesis. Application of this strategy led to a number of core fragments with no previously reported activity against kinases. Small libraries around the core fragments were synthesized, and representative compounds were tested against a large panel of protein kinases and subjected to co-crystallization experiments. Each of the tested compounds was active against at least one kinase, but not all kinases in the panel were inhibited. A number of compounds showed high ligand efficiencies for therapeutically relevant kinases; among them were MAPKAP-K3, SRPK1, SGK1, TAK1, and GCK for which only few inhibitors are reported in the literature.


    Organizational Affiliation

    Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Sir James Black Centre, DD1 5EH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusMutation(s): 0 
Gene Names: SRC
EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus)
Go to Gene View: SRC
Go to UniProtKB:  P00523
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0UL
Query on 0UL

Download SDF File 
Download CCD File 
A, B
6-phenyl[1,2,4]triazolo[1,5-a]pyrazin-2-amine
C11 H9 N5
NKIXJKQWFAULJD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0ULIC50: 20000 - 21000 nM (100) BINDINGDB
0ULIC50: 20000 nM BINDINGMOAD
0ULIC50: 20000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.034α = 79.63
b = 63.013β = 88.12
c = 73.561γ = 90.17
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-06-08 
  • Released Date: 2013-04-10 
  • Deposition Author(s): Richters, A., Rauh, D.

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references
  • Version 1.2: 2013-06-19
    Type: Database references