9XU9 | pdb_00009xu9

Crystal structure of EGFR T790M/C797S/L858R mutant in complex with (2-((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-yl)-5-nitrophenyl)amino)pyrimidin-4-yl)amino)phenyl)dimethylphosphine oxide

PDB DOI: https://doi.org/10.2210/pdb9XU9/pdb

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

Deposited: 2025-11-24 Released: 2025-12-24
Deposition Author(s): Wang, Y.Y., Ma, L.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free:
0.294 (Depositor), 0.294 (DCC)
R-Value Work:
0.228 (Depositor), 0.228 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of EGFR T790M/C797S/L858R mutant in complex with (2-((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-yl)-5-nitrophenyl)amino)pyrimidin-4-yl)amino)phenyl)dimethylphosphine oxide

Wang, Y.Y., Ma, L.L.

To be published.

Macromolecule Content

Total Structure Weight: 38.24 kDa
Atom Count: 2,472
Modeled Residue Count: 310
Deposited Residue Count: 331
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	331	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1E1C (Subject of Investigation/LOI) Query on A1E1C 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]	5-chloranyl-~{N}4-(2-dimethylphosphorylphenyl)-~{N}2-[2-methoxy-4-(4-methylpiperazin-1-yl)-5-nitro-phenyl]pyrimidine-2,4-diamine C₂₄ H₂₉ Cl N₇ O₄ P JPGNRNMUXAFODV-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: 2.84 Å
R-Value Free: 0.294 (Depositor), 0.294 (DCC)
R-Value Work: 0.228 (Depositor), 0.228 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.44	α = 90
b = 145.44	β = 90
c = 145.44	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

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: 2025-12-24
Type: Initial release

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.