3F3W

Drug resistant cSrc kinase domain in complex with inhibitor RL45 (Type II)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 

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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusMutation(s): 2 
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
1BU
Query on 1BU
Download SDF File 
Download CCD File 
A, B
1-{4-[(6-aminoquinazolin-4-yl)amino]phenyl}-3-[3-tert-butyl-1-(3-methylphenyl)-1H-pyrazol-5-yl]urea
1-[4-(6-Amino-quinazolin-4-ylamino)-phenyl]-3-(5-tert-butyl-2-m-tolyl-2H-pyrazol-3-yl)-urea
C29 H30 N8 O
ZKESOLNZMJUNTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1BUIC50: 21 - 34 nM (99) BINDINGDB
1BUKd: 73 nM (99) BINDINGDB
1BUIC50: 34 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.060α = 78.70
b = 63.690β = 87.02
c = 75.120γ = 89.96
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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