8TO3

EGFR(T790M/V948R) in complex with LN5461

• PDB DOI: https://doi.org/10.2210/pdb8TO3/pdb

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


• Deposited: 2023-08-02 Released: 2024-08-28 
• Deposition Author(s): Chitnis, S.C., Pham, C.D., Heppner, D.E.
• Funding Organization(s): National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.269 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Literature

EGFR(T790M/V948R) in complex with LN5461

Chitnis, S.P., Pham, C.D., Heppner, D.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 152.23 kDa 
• Atom Count: 9,648 
• Modelled Residue Count: 1,170 
• Deposited Residue Count: 1,312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A [auth D], B [auth A], C [auth B], D [auth C]	328	Homo sapiens	Mutation(s): 2  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IXC (Subject of Investigation/LOI)	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	F [auth D], I [auth B], K [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	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 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.999	α = 90
b = 73.369	β = 99.6
c = 150.591	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Chitnis, S.C., Pham, C.D., Heppner, D.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	United States	UL1TR001412

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release