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)

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
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Ligand Structure Quality Assessment

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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ECU (Subject of Investigation/LOI) Query on A1ECU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-02

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.