7KY0

Inactive conformation of EGFR (T790M/V948R) kinase in complex with BI-4020

• PDB DOI: https://doi.org/10.2210/pdb7KY0/pdb

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


• Deposited: 2020-12-06 Released: 2022-01-19 
• Deposition Author(s): Beyett, T.S., Eck, M.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.292 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

Structural analysis of the macrocyclic inhibitor BI-4020 binding to the active and inactive conformations of EGFR kinase

Beyett, T.S., Heppner, D.E., Rana, J., Eck, M.J.

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: 153.07 kDa 
• Atom Count: 9,491 
• Modelled Residue Count: 1,156 
• Deposited Residue Count: 1,324 
• 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]	331	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XA4 (Subject of Investigation/LOI)	E [auth D], F [auth A], G [auth B], H [auth C]	(20R)-10,15,20-trimethyl-2-[(4-methylpiperazin-1-yl)methyl]-18,19,20,21-tetrahydro-15H,17H-12,8-(metheno)pyrazolo[3',4':2,3][1,5,10,12]oxatriazacycloheptadecino[12,11-a]benzimidazol-7(6H)-one C30 H38 N8 O2 AIQBYZOTCIQTGW-HXUWFJFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.292 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.221	α = 90
b = 100.729	β = 101.07
c = 86.789	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Beyett, T.S., Eck, M.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R01CA116020-14
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2022-01-19
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description