9FZR | pdb_00009fzr

Wild-type EGFR in covalent complex with Poziotinib analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Factors affecting irreversible inhibition of EGFR and influence of chirality on covalent binding.

Morese, P.A.Ahmad, A.Martin, M.P.Noble, R.A.Pintar, S.Wang, L.Z.Xu, S.Lister, A.Ward, R.A.Bronowska, A.K.Noble, M.E.M.Stewart, H.L.Waring, M.J.

(2025) Commun Chem 8: 111-111

  • DOI: https://doi.org/10.1038/s42004-025-01501-6
  • Primary Citation of Related Structures:  
    9FZR, 9FZS

  • PubMed Abstract: 

    The discovery of targeted covalent inhibitors is of increasing importance in drug discovery. Finding efficient covalent binders requires modulation of warhead reactivity and optimisation of warhead geometry and non-covalent interactions. Uncoupling the contributions that these factors make to potency is difficult and best practice for a testing cascade that is pragmatic and informative is yet to be fully established. We studied the structure-reactivity-activity relationships of a series of analogues of the EGFR inhibitor poziotinib with point changes in two substructural regions as well as variations in warhead reactivity and geometry. This showed that a simple probe displacement assay that is appropriately tuned in respect of timing and reagent concentrations can reveal structural effects on all three factors: non-covalent affinity, warhead reactivity and geometry. These effects include the detection of potency differences between an enantiomeric pair that differ greatly in their activity and their capacity to form a covalent bond. This difference is rationalised by X-ray crystallography and computational studies and the effect translates quantitatively into cellular mechanistic and phenotypic effects.


  • Organizational Affiliation
    • Cancer Research Horizons Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor329Homo sapiensMutation(s): 0 
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
A1IHC (Subject of Investigation/LOI)
Query on A1IHC

Download Ideal Coordinates CCD File 
B [auth A]1-[(3~{S})-3-[4-[(3-chloranyl-4-fluoranyl-phenyl)amino]-7-methoxy-quinazolin-6-yl]oxypyrrolidin-1-yl]propan-1-one
C22 H22 Cl F N4 O3
GBUJQSIKHBSPDW-AWEZNQCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.823α = 90
b = 145.823β = 90
c = 145.823γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC2115/A21421
Engineering and Physical Sciences Research CouncilUnited KingdomEP/R51309X/1
Cancer Research UKUnited KingdomDRCDDRPGMApr2020100002

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references