5FED

EGFR kinase domain in complex with a covalent aminobenzimidazole inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.651 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of (R,E)-N-(7-Chloro-1-(1-[4-(dimethylamino)but-2-enoyl]azepan-3-yl)-1H-benzo[d]imidazol-2-yl)-2-methylisonicotinamide (EGF816), a Novel, Potent, and WT Sparing Covalent Inhibitor of Oncogenic (L858R, ex19del) and Resistant (T790M) EGFR Mutants for the Treatment of EGFR Mutant Non-Small-Cell Lung Cancers.

Lelais, G.Epple, R.Marsilje, T.H.Long, Y.O.McNeill, M.Chen, B.Lu, W.Anumolu, J.Badiger, S.Bursulaya, B.DiDonato, M.Fong, R.Juarez, J.Li, J.Manuia, M.Mason, D.E.Gordon, P.Groessl, T.Johnson, K.Jia, Y.Kasibhatla, S.Li, C.Isbell, J.Spraggon, G.Bender, S.Michellys, P.Y.

(2016) J.Med.Chem. 59: 6671-6689

  • DOI: 10.1021/acs.jmedchem.5b01985
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Over the past decade, first and second generation EGFR inhibitors have significantly improved outcomes for lung cancer patients with activating mutations in EGFR. However, both resistance through a secondary T790M mutation at the gatekeeper residue a ...

    Over the past decade, first and second generation EGFR inhibitors have significantly improved outcomes for lung cancer patients with activating mutations in EGFR. However, both resistance through a secondary T790M mutation at the gatekeeper residue and dose-limiting toxicities from wild-type (WT) EGFR inhibition ultimately limit the full potential of these therapies to control mutant EGFR-driven tumors and new therapies are urgently needed. Herein, we describe our approach toward the discovery of 47 (EGF816, nazartinib), a novel, covalent mutant-selective EGFR inhibitor with equipotent activity on both oncogenic and T790M-resistant EGFR mutations. Through molecular docking studies we converted a mutant-selective high-throughput screening hit (7) into a number of targeted covalent EGFR inhibitors with equipotent activity across mutants EGFR and good WT-EGFR selectivity. We used an abbreviated in vivo efficacy study for prioritizing compounds with good tolerability and efficacy that ultimately led to the selection of 47 as the clinical candidate.


    Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation , 10675 John J. Hopkins Drive, San Diego, California 92121, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A
328Homo sapiensMutation(s): 0 
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
5X4
Query on 5X4

Download SDF File 
Download CCD File 
A
~{N}-[7-methyl-1-[(3~{R})-1-propanoylazepan-3-yl]benzimidazol-2-yl]-3-(trifluoromethyl)benzamide
C25 H27 F3 N4 O2
DFNLNAPTJYVZSV-LJQANCHMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.651 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 145.584α = 90.00
b = 145.584β = 90.00
c = 145.584γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references