5UWD

Crystal structure of EGFR kinase domain (L858R, T790M, V948R) in complex with the covalent inhibitor CO-1686


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Proteome-wide Map of Targets of T790M-EGFR-Directed Covalent Inhibitors.

Niessen, S.Dix, M.M.Barbas, S.Potter, Z.E.Lu, S.Brodsky, O.Planken, S.Behenna, D.Almaden, C.Gajiwala, K.S.Ryan, K.Ferre, R.Lazear, M.R.Hayward, M.M.Kath, J.C.Cravatt, B.F.

(2017) Cell Chem Biol 24: 1388-1400.e7

  • DOI: 10.1016/j.chembiol.2017.08.017

  • PubMed Abstract: 
  • Patients with non-small cell lung cancers that have kinase-activating epidermal growth factor receptor (EGFR) mutations are highly responsive to first- and second-generation EGFR inhibitors. However, these patients often relapse due to a secondary, d ...

    Patients with non-small cell lung cancers that have kinase-activating epidermal growth factor receptor (EGFR) mutations are highly responsive to first- and second-generation EGFR inhibitors. However, these patients often relapse due to a secondary, drug-resistant mutation in EGFR whereby the gatekeeper threonine is converted to methionine (T790M). Several third-generation EGFR inhibitors have been developed that irreversibly inactivate T790M-EGFR while sparing wild-type EGFR, thus reducing epithelium-based toxicities. Using chemical proteomics, we show here that individual T790M-EGFR inhibitors exhibit strikingly distinct off-target profiles in human cells. The FDA-approved drug osimertinib (AZD9291), in particular, was found to covalently modify cathepsins in cell and animal models, which correlated with lysosomal accumulation of the drug. Our findings thus show how chemical proteomics can be used to differentiate covalent kinase inhibitors based on global selectivity profiles in living systems and identify specific off-targets of these inhibitors that may affect drug activity and safety.


    Organizational Affiliation

    Worldwide Medicinal Chemistry, La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, CA 92121, USA; Oncology RU, La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, CA 92121, USA. Electronic address: sherry.niessen@pfizer.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A
329Homo sapiensMutation(s): 3 
Gene Names: EGFR (ERBB, ERBB1, HER1)
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Go to Gene View: EGFR
Go to UniProtKB:  P00533
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8OV
Query on 8OV

Download SDF File 
Download CCD File 
A
N-(3-{[2-{[4-(4-acetylpiperazin-1-yl)-2-methoxyphenyl]amino}-5-(trifluoromethyl)pyrimidin-4-yl]amino}phenyl)propanamide
C27 H30 F3 N7 O3
XRXFHVJORXTVSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.213 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.926α = 90.00
b = 78.926β = 90.00
c = 215.596γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references