Download MendeleyComprehensive characterization of EGFR-tyrosine kinase inhibitor interactions probed by hydrogen-deuterium exchange and mass spectrometry (HDX-MS)
Tsutsui, Y., Ashtekar, K.D., Stayrook, S., Lemmon, M.A.To be published.
9BY4 | pdb_00009by4
Co-crystal structure of the kinase domain of EGFR with non-covalent osimertinib
- PDB DOI: https://doi.org/10.2210/pdb9BY4/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2024-05-23 Released: 2025-05-28
- Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.31 Å
- R-Value Free: 0.220 (Depositor), 0.225 (DCC)
- R-Value Work: 0.196 (Depositor), 0.202 (DCC)
- R-Value Observed: 0.197 (Depositor)
Starting Model: experimental
View more details
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Epidermal growth factor receptor | 338 | Homo sapiens | Mutation(s): 0 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 AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| Q6K (Subject of Investigation/LOI) Query on Q6K | C [auth A] | ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide C28 H35 N7 O2 UHTBXBRYOKJTAN-UHFFFAOYSA-N |  | ||
| PDO Query on PDO | B [auth A], E [auth A], F [auth A] | 1,3-PROPANDIOL C3 H8 O2 YPFDHNVEDLHUCE-UHFFFAOYSA-N |  | ||
| CA Query on CA | D [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.31 Å
- R-Value Free: 0.220 (Depositor), 0.225 (DCC)
- R-Value Work: 0.196 (Depositor), 0.202 (DCC)
- R-Value Observed: 0.197 (Depositor)
Space Group: I 2 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 145.968 | α = 90 |
| b = 145.968 | β = 90 |
| c = 145.968 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALA | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-05-28 Deposition Author(s): Ashtekar, K.D., Stayrook, S.E., Lemmon, M.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Cancer Institute (NIH/NCI) | United States | GR110199 |
Revision History (Full details and data files)
- Version 1.0: 2025-05-28
Type: Initial release - Version 1.1: 2025-10-01
Changes: Data collection
