Crystal Structure of EGFR-T790M/C797S in Complex with Covalent Pyrrolopyrimidine 19h

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Inhibition of osimertinib-resistant epidermal growth factor receptor EGFR-T790M/C797S.

Lategahn, J.Keul, M.Klovekorn, P.Tumbrink, H.L.Niggenaber, J.Muller, M.P.Hodson, L.Flasshoff, M.Hardick, J.Grabe, T.Engel, J.Schultz-Fademrecht, C.Baumann, M.Ketzer, J.Muhlenberg, T.Hiller, W.Gunther, G.Unger, A.Muller, H.Heimsoeth, A.Golz, C.Blank-Landeshammer, B.Kollipara, L.Zahedi, R.P.Strohmann, C.Hengstler, J.G.van Otterlo, W.A.L.Bauer, S.Rauh, D.

(2019) Chem Sci 10: 10789-10801

  • DOI: https://doi.org/10.1039/c9sc03445e
  • Primary Citation of Related Structures:  
    6HVE, 6HVF, 6S89, 6S8A

  • PubMed Abstract: 

    Precision medicine has revolutionized the treatment of patients in EGFR driven non-small cell lung cancer (NSCLC). Targeted drugs show high response rates in genetically defined subsets of cancer patients and markedly increase their progression-free survival as compared to conventional chemotherapy. However, recurrent acquired drug resistance limits the success of targeted drugs in long-term treatment and requires the constant development of novel efficient inhibitors of drug resistant cancer subtypes. Herein, we present covalent inhibitors of the drug resistant gatekeeper mutant EGFR-L858R/T790M based on the pyrrolopyrimidine scaffold. Biochemical and cellular characterization, as well as kinase selectivity profiling and western blot analysis, substantiate our approach. Moreover, the developed compounds possess high activity against multi drug resistant EGFR-L858R/T790M/C797S in biochemical assays due to their highly reversible binding character, that was revealed by characterization of the binding kinetics. In addition, we present the first X-ray crystal structures of covalent inhibitors in complex with C797S-mutated EGFR which provide detailed insight into their binding mode.

  • Organizational Affiliation

    Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . Email: daniel.rauh@tu-dortmund.de ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor333Homo sapiensMutation(s): 5 
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens)
Explore P00533 
Go to UniProtKB:  P00533
PHAROS:  P00533
GTEx:  ENSG00000146648 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L0N (Subject of Investigation/LOI)
Query on L0N

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[3-[6-[4-(4-methylpiperazin-1-yl)phenyl]-4-(2-methylpropoxy)-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]phenyl]propanamide
C30 H36 N6 O2
Query on MES

Download Ideal Coordinates CCD File 
C6 H13 N O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142α = 90
b = 142β = 90
c = 142γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanyBMBF 01GS08104
German Federal Ministry for Education and ResearchGermanyBMBF 01ZX1303C
European Regional Development FundGermanyEFRE-800400

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description