7JXM | pdb_00007jxm

EGFR kinase (T790M/V948R) in complex with osimertinib and EAI045

PDB DOI: https://doi.org/10.2210/pdb7JXM/pdb

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

Deposited: 2020-08-27 Released: 2021-09-08
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: 2.19 Å
R-Value Free:
0.271 (Depositor), 0.268 (DCC)
R-Value Work:
0.227 (Depositor), 0.229 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors

Beyett, T.S., To, C., Heppner, D.E., Rana, J.K., Schmoker, A.M., Jang, J., De Clercq, D.J.H., Gomez, G., Scott, D.A., Gray, N.S., Janne, P.A., Eck, M.J.

(2022) Nat Commun 13: 2530

DOI: https://doi.org/10.1038/s41467-022-30258-y

Macromolecule Content

Total Structure Weight: 153.76 kDa
Atom Count: 9,753
Modeled Residue Count: 1,159
Deposited Residue Count: 1,324
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A [auth D], B [auth A], C, D [auth B]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain J [auth C] SDF format, chain H [auth A] MOL2 format, chain E [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth A] mmCIF format, chain E [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth A]	E [auth D], H [auth A], J [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain E [auth D] Focus chain H [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth D] Focus chain H [auth A] Focus chain J [auth C]
YY3 (Subject of Investigation/LOI) Query on YY3 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide C₂₈ H₃₃ N₇ O₂ DUYJMQONPNNFPI-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
9LL (Subject of Investigation/LOI) Query on 9LL Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain M [auth B] MOL2 format, chain G [auth D] MOL2 format, chain M [auth B] mmCIF format, chain G [auth D] mmCIF format, chain M [auth B]	G [auth D], M [auth B]	(2R)-2-(5-fluoro-2-hydroxyphenyl)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-N-(1,3-thiazol-2-yl)acetamide C₁₉ H₁₄ F N₃ O₃ S YTUFHOKUFOQRDF-MRXNPFEDSA-N		Interactions Focus chain G [auth D] Focus chain M [auth B] Interactions & Density Focus chain G [auth D] Focus chain M [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain I [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] mmCIF format, chain F [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C]	F [auth D], I [auth A], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain I [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth D] Focus chain I [auth A] Focus chain K [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
9LL	BindingDB: 7JXM	IC50: min: 2, max: 1.50e+4 (nM) from 16 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.271 (Depositor), 0.268 (DCC)
R-Value Work: 0.227 (Depositor), 0.229 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.548	α = 90
b = 103.224	β = 101.55
c = 87.043	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-08

Deposition Author(s):

Beyett, T.S.

Eck, M.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R01CA201049-05
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1F32CA247198-01