3G5D

Kinase domain of cSrc in complex with Dasatinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hybrid compound design to overcome the gatekeeper T338M mutation in cSrc

Getlik, M.Grutter, C.Simard, J.R.Kluter, S.Rabiller, M.Rode, H.B.Robubi, A.Rauh, D.

(2009) J Med Chem 52: 3915-3926

  • DOI: 10.1021/jm9002928
  • Primary Citation of Related Structures:  
    3G5D, 3F3V, 3F3W

  • PubMed Abstract: 
  • The emergence of drug resistance remains a fundamental challenge in the development of kinase inhibitors that are effective over long-term treatments. Allosteric inhibitors that bind to sites lying outside the highly conserved ATP pocket are thought to be more selective than ATP-competitive inhibitors and may circumvent some mechanisms of drug resistance ...

    The emergence of drug resistance remains a fundamental challenge in the development of kinase inhibitors that are effective over long-term treatments. Allosteric inhibitors that bind to sites lying outside the highly conserved ATP pocket are thought to be more selective than ATP-competitive inhibitors and may circumvent some mechanisms of drug resistance. Crystal structures of type I and allosteric type III inhibitors in complex with the tyrosine kinase cSrc allowed us to employ principles of structure-based design to develop these scaffolds into potent type II kinase inhibitors. One of these compounds, 3c (RL46), disrupts FAK-mediated focal adhesions in cancer cells via direct inhibition of cSrc. Details gleaned from crystal structures revealed a key feature of a subset of these compounds, a surprising flexibility in the vicinity of the gatekeeper residue that allows these compounds to overcome a dasatinib-resistant gatekeeper mutation emerging in cSrc.


    Organizational Affiliation

    Chemical Genomics Centre of the Max Planck Society, D-44227 Dortmund, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src AB286Gallus gallusMutation(s): 1 
Gene Names: SRC
EC: 2.7.10.2
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N1
Query on 1N1

Download Ideal Coordinates CCD File 
A, B
N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
C22 H26 Cl N7 O2 S
ZBNZXTGUTAYRHI-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1N1IC50:  14   nM  BindingDB
1N1Kd:  0.30000001192092896   nM  BindingDB
1N1IC50:  0.3999999761581421   nM  Binding MOAD
1N1IC50:  0.4000000059604645   nM  BindingDB
1N1IC50:  10   nM  BindingDB
1N1Kd:  0.07000000029802322   nM  BindingDB
1N1Kd:  11   nM  BindingDB
1N1IC50:  0.5   nM  BindingDB
1N1Kd :  11   nM  PDBBind
1N1IC50:  10   nM  BindingDB
1N1IC50:  0.30000001192092896   nM  BindingDB
1N1IC50:  0.5   nM  BindingDB
1N1IC50:  0.5   nM  BindingDB
1N1Kd:  0.20999999344348907   nM  BindingDB
1N1IC50:  0.5   nM  BindingDB
1N1IC50:  1   nM  BindingDB
1N1IC50:  0.6000000238418579   nM  BindingDB
1N1IC50:  1.5   nM  BindingDB
1N1IC50:  1   nM  BindingDB
1N1IC50:  480   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.19α = 78.71
b = 63.69β = 89.96
c = 74.58γ = 90.28
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance