7UKV

Wild type EGFR in complex with Lazertinib (YH25448)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Inhibition of Mutant EGFR with Lazertinib (YH25448).

Heppner, D.E.Wittlinger, F.Beyett, T.S.Shaurova, T.Urul, D.A.Buckley, B.Pham, C.D.Schaeffner, I.K.Yang, B.Ogboo, B.C.May, E.W.Schaefer, E.M.Eck, M.J.Laufer, S.A.Hershberger, P.A.

(2022) ACS Med Chem Lett 13: 1856-1863

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00213
  • Primary Citation of Related Structures:  
    7UKV, 7UKW

  • PubMed Abstract: 

    Lazertinib (YH25448) is a novel third-generation tyrosine kinase inhibitor (TKI) developed as a treatment for EGFR mutant non-small cell lung cancer. To better understand the nature of lazertinib inhibition, we determined crystal structures of lazertinib in complex with both WT and mutant EGFR and compared its binding mode to that of structurally related EGFR TKIs. We observe that lazertinib binds EGFR with a distinctive pyrazole moiety enabling hydrogen bonds and van der Waals interactions facilitated through hydrophilic amine and hydrophobic phenyl groups, respectively. Biochemical assays and cell studies confirm that lazertinib effectively targets EGFR(L858R/T790M) and to a lesser extent HER2. The molecular basis for lazertinib inhibition of EGFR reported here highlights previously unexplored binding interactions leading to improved medicinal chemistry properties compared to clinically approved osimertinib (AZD9291) and offers novel strategies for structure-guided design of tyrosine kinase inhibitors.


  • Organizational Affiliation

    Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptor328Homo 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
ZRT (Subject of Investigation/LOI)
Query on ZRT

Download Ideal Coordinates CCD File 
B [auth A]N-[5-{[(4P)-4-{4-[(dimethylamino)methyl]-3-phenyl-1H-pyrazol-1-yl}pyrimidin-2-yl]amino}-4-methoxy-2-(morpholin-4-yl)phenyl]propanamide
C30 H36 N8 O3
JCMFJBUWEYTTAQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.7α = 90
b = 145.7β = 90
c = 145.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA116020
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA201049
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR35CA242461
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesF32CA247198

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description