7ZYM

Crystal Structure of EGFR-T790M/C797S in Complex with Brigatinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Addressing the Osimertinib Resistance Mutation EGFR-L858R/C797S with Reversible Aminopyrimidines.

Grabe, T.Jeyakumar, K.Niggenaber, J.Schulz, T.Koska, S.Kleinbolting, S.Beck, M.E.Muller, M.P.Rauh, D.

(2023) ACS Med Chem Lett 14: 591-598

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00514
  • Primary Citation of Related Structures:  
    7ZYM, 7ZYN, 7ZYP, 7ZYQ

  • PubMed Abstract: 

    Drug resistance mutations emerging during the treatment of non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) inhibitors represent a major challenge in personalized cancer treatment and require constant development of new inhibitors. For the covalent irreversible EGFR inhibitor osimertinib, the predominant resistance mechanism is the acquired C797S mutation, which abolishes the covalent anchor point and thus results in a dramatic loss in potency. In this study, we present next-generation reversible EGFR inhibitors with the potential to overcome this EGFR-C797S resistance mutation. For this, we combined the reversible methylindole-aminopyrimidine scaffold known from osimertinib with the affinity driving isopropyl ester of mobocertinib. By occupying the hydrophobic back pocket, we were able to generate reversible inhibitors with subnanomolar activity against EGFR-L858R/C797S and EGFR-L858R/T790M/C797S with cellular activity on EGFR-L858R/C797S dependent Ba/F3 cells. Additionally, we were able to resolve cocrystal structures of these reversible aminopyrimidines, which will guide further inhibitor design toward C797S-mutated EGFR.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor333Homo sapiensMutation(s): 5 
Gene Names: EGFRERBBERBB1HER1
EC: 2.7.10.1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6GY (Subject of Investigation/LOI)
Query on 6GY

Download Ideal Coordinates CCD File 
B [auth A]5-chloro-N~4~-[2-(dimethylphosphoryl)phenyl]-N~2~-{2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl}pyrimidine-2,4-diamine
C29 H39 Cl N7 O2 P
AILRADAXUVEEIR-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6GY BindingDB:  7ZYM IC50: min: 0.7, max: 1700 (nM) from 37 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.1α = 90
b = 146.1β = 90
c = 146.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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 FundEuropean UnionEFRE-800400

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Structure summary
  • Version 1.2: 2023-05-31
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description