8TO3 | pdb_00008to3

EGFR(T790M/V948R) in complex with LN5461


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.269 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IXCClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Tilting the Scales toward EGFR Mutant Selectivity: Expanding the Scope of Bivalent "Type V" Kinase Inhibitors.

Wittlinger, F.Chitnis, S.P.Pham, C.D.Damghani, T.Patel, K.B.Mollers, M.Schaeffner, I.K.Abidakun, O.A.Deng, M.Q.Ogboo, B.C.Rasch, A.Beyett, T.S.Buckley, B.Feru, F.Shaurova, T.Knappe, C.Eck, M.J.Hershberger, P.A.Scott, D.A.Brandt, A.L.Laufer, S.A.Heppner, D.E.

(2024) J Med Chem 67: 21438-21469

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02311
  • Primary Citation of Related Structures:  
    8TO3, 8TO4

  • PubMed Abstract: 

    Binding multiple sites within proteins with bivalent compounds is a strategy for developing uniquely active agents. A new class of dual-site inhibitors has emerged targeting the epidermal growth factor receptor (EGFR) anchored to both the orthosteric (ATP) and allosteric sites. Despite proof-of-concept successes, enabling selectivity against oncogenic activating mutations has not been achieved and classifying these inhibitors among kinase inhibitors remains underexplored. This study investigates the structure-activity relationships, binding modes, and biological activity of ATP-allosteric bivalent inhibitors (AABIs). We find that AABIs selectively inhibit drug-resistant EGFR mutants (L858R/T790M and L858R/T790M/C797S) by anchoring a methyl isoindolinone moiety along the αC-helix channel of the allosteric site. In contrast, related Type I 1 / 2 inhibitors target wild-type EGFR but are less effective against resistant mutants. This shift in selectivity demonstrates that mutant-selective AABIs classify as "Type V" bivalent inhibitors.


  • Organizational Affiliation

    Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptorA [auth D],
B [auth A],
C [auth B],
D [auth C]
328Homo sapiensMutation(s): 2 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IXC (Subject of Investigation/LOI)
Query on IXC

Download Ideal Coordinates CCD File 
G [auth A]3-hydroxy-N-{(3P)-3-[(4P)-2-(methylsulfanyl)-5-{2-[4-(piperazin-1-yl)anilino]pyridin-4-yl}-1H-imidazol-4-yl]phenyl}-2-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]benzamide
C41 H38 N8 O3 S
DBLFPZMZQSDENE-UHFFFAOYSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
F [auth D],
I [auth B],
K [auth C]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth D],
H [auth B],
J [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.269 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.999α = 90
b = 73.369β = 99.6
c = 150.591γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IXCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesUL1TR001412

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Database references, Structure summary