6LUD | pdb_00006lud

Crystal Structure of EGFR(L858R/T790M/C797S) in complex with Osimertinib

• PDB DOI: https://doi.org/10.2210/pdb6LUD/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2020-01-27 Released: 2020-10-07 
• Deposition Author(s): Kawauchi, H., Fukami, T.A., Sato, S., Endo, M., Torizawa, T., Kashima, K., Chiba, T., Sakamoto, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

CH7233163 Overcomes Osimertinib-Resistant EGFR-Del19/T790M/C797S Mutation.

Kashima, K., Kawauchi, H., Tanimura, H., Tachibana, Y., Chiba, T., Torizawa, T., Sakamoto, H.

(2020) Mol Cancer Ther 19: 2288-2297

• PubMed: 32943545 
• DOI: https://doi.org/10.1158/1535-7163.MCT-20-0229
• Primary Citation Related Structures: 
  6LUB, 6LUD


• PubMed Abstract: 
  

  Osimertinib is the only EGFR-tyrosine kinase inhibitor (TKI) capable of overcoming EGFR-T790M-mutated NSCLC, but osimertinib-resistant EGFR triple mutations (Del19/T790M/C797S or L858R/T790M/C797S) have been reported. Although allosteric EGFR TKIs (e.g., EAI-045) that potentially overcome L858R/T790M/C797S have been identified, there are no effective inhibitors against Del19/T790M/C797S. In this study, we identified CH7233163 as having the potential to overcome EGFR-Del19/T790M/C797S. CH7233163 showed potent antitumor activities against tumor with EGFR-Del19/T790M/C797S in vitro and in vivo In addition to EGFR-Del19/T790M/C797S, the characterization assays showed that CH7233163 more selectively inhibits various types of EGFR mutants (e.g., L858R/T790M/C797S, L858R/T790M, Del19/T790M, Del19, and L858R) over wild type. Furthermore, crystal structure analysis suggested that CH7233163 is a noncovalent ATP-competitive inhibitor for EGFR-Del19/T790M/C797S that utilizes multiple interactions with the EGFR's αC-helix-in conformation to achieve potent inhibitory activity and mutant selectivity. Therefore, we conclude that CH7233163 is a potentially effective therapy for osimertinib-resistant patients, especially in cases of EGFR-Del19/T790M/C797S.

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Organizational Affiliation: 
• Research Division, Chugai Pharmaceutical Co. Ltd., Kanagawa, Japan. [e-mail].
Research Division, Chugai Pharmaceutical Co. Ltd., Kanagawa, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.83 kDa 
• Atom Count: 2,478 
• Modeled Residue Count: 310 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	329	Homo sapiens	Mutation(s): 6  Gene Names: EGFR, ERBB, ERBB1, HER1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YY3 (Subject of Investigation/LOI)	B [auth A]	N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide C28 H33 N7 O2 DUYJMQONPNNFPI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.932	α = 90
b = 143.932	β = 90
c = 143.932	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
DIMPLE	phasing
autoPROC	data scaling
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Kawauchi, H., Fukami, T.A., Sato, S., Endo, M., Torizawa, T., Kashima, K., Chiba, T., Sakamoto, H.

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2021-08-25
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description