8HY7 | pdb_00008hy7

EGFR kinase domain mutant "TMLR" with compound 28f

PDB DOI: https://doi.org/10.2210/pdb8HY7/pdb

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

Deposited: 2023-01-06 Released: 2023-08-23
Deposition Author(s): Wang, Y.X., Wu, C.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free:
0.251 (Depositor), 0.250 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8HY7

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of EGFR kinase domain(T790M/L858R) in complex with compound 28f

Wang, Y.X., Wu, C.Y.

To be published.

Macromolecule Content

Total Structure Weight: 37.99 kDa
Atom Count: 2,437
Modeled Residue Count: 299
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	330	Homo sapiens	Mutation(s): 5 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
NSO (Subject of Investigation/LOI) Query on NSO 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]	~{N}-[3-[[6-fluoranyl-2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]quinazolin-4-yl]amino]phenyl]prop-2-enamide C₂₈ H₂₈ F N₇ O KDWNVZXLHSMELQ-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: 2.91 Å
R-Value Free: 0.251 (Depositor), 0.250 (DCC)
R-Value Work: 0.195 (Depositor), 0.195 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.2	α = 90
b = 146.2	β = 90
c = 146.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoXDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-23
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.