5D11

Kinase domain of cSrc in complex with RL235


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach.

Engel, J.Richters, A.Getlik, M.Tomassi, S.Keul, M.Termathe, M.Lategahn, J.Becker, C.Mayer-Wrangowski, S.Grutter, C.Uhlenbrock, N.Krull, J.Schaumann, N.Eppmann, S.Kibies, P.Hoffgaard, F.Heil, J.Menninger, S.Ortiz-Cuaran, S.Heuckmann, J.M.Tinnefeld, V.Zahedi, R.P.Sos, M.L.Schultz-Fademrecht, C.Thomas, R.K.Kast, S.M.Rauh, D.

(2015) J.Med.Chem. 58: 6844-6863

  • DOI: 10.1021/acs.jmedchem.5b01082
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Receptor tyrosine kinases represent one of the prime targets in cancer therapy, as the dysregulation of these elementary transducers of extracellular signals, like the epidermal growth factor receptor (EGFR), contributes to the onset of cancer, such ...

    Receptor tyrosine kinases represent one of the prime targets in cancer therapy, as the dysregulation of these elementary transducers of extracellular signals, like the epidermal growth factor receptor (EGFR), contributes to the onset of cancer, such as non-small cell lung cancer (NSCLC). Strong efforts were directed to the development of irreversible inhibitors and led to compound CO-1686, which takes advantage of increased residence time at EGFR by alkylating Cys797 and thereby preventing toxic effects. Here, we present a structure-based approach, rationalized by subsequent computational analysis of conformational ligand ensembles in solution, to design novel and irreversible EGFR inhibitors based on a screening hit that was identified in a phenotype screen of 80 NSCLC cell lines against approximately 1500 compounds. Using protein X-ray crystallography, we deciphered the binding mode in engineered cSrc (T338M/S345C), a validated model system for EGFR-T790M, which constituted the basis for further rational design approaches. Chemical synthesis led to further compound collections that revealed increased biochemical potency and, in part, selectivity toward mutated (L858R and L858R/T790M) vs nonmutated EGFR. Further cell-based and kinetic studies were performed to substantiate our initial findings. Utilizing proteolytic digestion and nano-LC-MS/MS analysis, we confirmed the alkylation of Cys797.


    Organizational Affiliation

    Molecular Pathology, University Hospital of Cologne , Kerpenerstraße 62, D-50937 Cologne, Germany.,Chemical Genomics Centre of the Max-Planck Society , Otto-Hahn-Straße 15, D-44227 Dortmund, Germany.,Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , D-44139 Dortmund, Germany.,Lead Discovery Center GmbH , Otto-Hahn-Straße 15, D-44227 Dortmund, Germany.,Department of Pathology, University of Cologne , Joseph-Stelzmann Straße 9, D-50931 Cologne, Germany.,Department of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Straße 6, D-44227 Dortmund, Germany.,Department of Translational Genomics, Medical Faculty, University of Cologne , Weyertal 115b, D-50931 Cologne, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
56G
Query on 56G

Download SDF File 
Download CCD File 
A, B
N-[3-({4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}oxy)phenyl]prop-2-enamide
C22 H26 N8 O2
PSWJMRDJPWAQDI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
56GIC50: 28 - 170 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.120α = 78.65
b = 63.430β = 89.55
c = 75.350γ = 90.29
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references