9JQ1 | pdb_00009jq1

Crystal structure of EGFR T790M/C797S/L858R mutant in complex with 2,2-dichloro-N-(5-((5-chloro-4-((2-(dimethylphosphoryl)phenyl)amino)pyrimidin-2-yl)amino)-4-methoxy-2-(4-(4-methylpiperazin-1-yl)piperidin-1-yl)phenyl)acetamide

• PDB DOI: https://doi.org/10.2210/pdb9JQ1/pdb

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


• Deposited: 2024-09-27 Released: 2025-07-02 
• Deposition Author(s): Wang, Y., Ma, L., Yang, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of EGFR T790M/C797S/L858R mutant in complex with 2,2-dichloro-N-(5-((5-chloro-4-((2-(dimethylphosphoryl)phenyl)amino)pyrimidin-2-yl)amino)-4-methoxy-2-(4-(4-methylpiperazin-1-yl)piperidin-1-yl)phenyl)acetamide

Wang, Y., Ma, L., Yang, X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.22 kDa 
• Atom Count: 2,450 
• Modeled Residue Count: 301 
• 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): 3  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
A1ECU (Subject of Investigation/LOI)	B [auth A]	2,2-bis(chloranyl)-~{N}-[5-[[5-chloranyl-4-[(2-dimethylphosphorylphenyl)amino]pyrimidin-2-yl]amino]-4-methoxy-2-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]ethanamide C31 H40 Cl3 N8 O3 P WKUTZQYPDRJNAE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.01	α = 90
b = 146.01	β = 90
c = 146.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building
PHASER	phasing
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Wang, Y., Ma, L., Yang, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82373721

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release