8GK5

EGFR(T790M/V948R) kinase in complex with osimertinib and benzimidazole allosteric inhibitor

PDB DOI: https://doi.org/10.2210/pdb8GK5/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2023-03-17 Released: 2024-06-26
Deposition Author(s): Beyett, T.S., Eck, M.J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.252
R-Value Work: 0.222
R-Value Observed: 0.224

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Development of benzimidazole allosteric EGFR kinase inhibitors

Beyett, T.S., Eck, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 155.03 kDa
Atom Count: 9,905
Modelled Residue Count: 1,173
Deposited Residue Count: 1,324
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, B, C, D	331	Homo sapiens	Mutation(s): 2 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YW5 (Subject of Investigation/LOI) Query on YW5 Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B], J [auth C], L [auth D]	2-[(R)-(1H-benzimidazol-2-yl)(3-fluorophenyl)methyl]-6-[4-(1-methylpiperidin-4-yl)phenyl]-2,3-dihydro-1H-isoindol-1-one C₃₄ H₃₁ F N₄ O ZMKPSKAUYOLPIA-JGCGQSQUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
Q6K (Subject of Investigation/LOI) Query on Q6K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	~{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		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]