Crystal structure of drug resistant SRC kinase domain with irreversible inhibitor

Experimental Data Snapshot

  • Resolution: 2.38 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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Structural insights into how irreversible inhibitors can overcome drug resistance in EGFR.

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

(2008) Bioorg Med Chem 16: 3482-3488

  • DOI: https://doi.org/10.1016/j.bmc.2008.02.053
  • Primary Citation of Related Structures:  
    2QI8, 2QLQ, 2QQ7

  • PubMed Abstract: 

    Resistance to kinase-targeted cancer drugs has recently been linked to a single point mutation in the ATP binding site of the kinase. In EGFR, the crucial Thr790 gatekeeper residue is mutated to a Met and prevents reversible ATP competitive inhibitors from binding. Irreversible 4-(phenylamino)quinazolines have been shown to overcome this drug resistance and are currently in clinical trials. In order to obtain a detailed structural understanding of how irreversible inhibitors overcome drug resistance, we used Src kinase as a model system for drug resistant EGFR-T790M. We report the first crystal structure of a drug resistant kinase in complex with an irreversible inhibitor. This 4-(phenylamino)quinazoline inhibits wild type and drug resistant EGFR in vitro at low nM concentrations. The co-crystal structure of drug resistant cSrc-T338M kinase domain provides the structural basis of this activity.

  • Organizational Affiliation

    Chemical Genomics Centre of the Max-Planck-Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusMutation(s): 2 
Gene Names: SRC
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00523
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SR2

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H20 Br N5 O
Binding Affinity Annotations 
IDSourceBinding Affinity
SR2 PDBBind:  2QQ7 IC50: 5710 (nM) from 1 assay(s)
BindingDB:  2QQ7 IC50: min: 236, max: 2.70e+4 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.38 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.22α = 78.58
b = 63.36β = 89.08
c = 75.06γ = 89.87
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations