7JXI | pdb_00007jxi

EGFR kinase (T790M/V948R) in complex with PF-06747775

• PDB DOI: https://doi.org/10.2210/pdb7JXI/pdb

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


• Deposited: 2020-08-27 Released: 2021-09-08 
• 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: 3.00 Å
• R-Value Free: 
  0.312 (Depositor), 0.314 (DCC) 
• R-Value Work: 
  0.276 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.278 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors

Beyett, T.S., To, C., Heppner, D.E., Rana, J.K., Schmoker, A.M., Jang, J., De Clercq, D.J.H., Gomez, G., Scott, D.A., Gray, N.S., Janne, P.A., Eck, M.J.

(2022) Nat Commun 13: 2530

• DOI: https://doi.org/10.1038/s41467-022-30258-y

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 152.57 kDa 
• Atom Count: 9,311 
• Modeled Residue Count: 1,136 
• 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, D [auth B]	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
8BS (Subject of Investigation/LOI)	E [auth D], F [auth A], G [auth C], H [auth B]	N-[(3R,4R)-4-fluoro-1-{6-[(3-methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-methyl-9H-purin-2-yl}pyrrolidin-3-yl]propanamide C18 H24 F N9 O2 XWNKXCUQRQRAFF-GHMZBOCLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.312 (Depositor), 0.314 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.278 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.63	α = 90
b = 100.778	β = 101.17
c = 87.155	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-08 
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	5R01CA201049-05
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1F32CA247198-01

Revision History  

• Version 1.0: 2021-09-08
  Type: Initial release
  
• Version 1.1: 2022-05-18
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary