7JXH | pdb_00007jxh

HER2 in complex with JBJ-08-178-01

PDB DOI: https://doi.org/10.2210/pdb7JXH/pdb

Classification: TRANSFERASE/TRANSFERASE Inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

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: 3.27 Å
R-Value Free:
0.285 (Depositor), 0.285 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A Novel HER2-Selective Kinase Inhibitor Is Effective in HER2 Mutant and Amplified Non-Small Cell Lung Cancer.

Son, J., Jang, J., Beyett, T.S., Eum, Y., Haikala, H.M., Verano, A., Lin, M., Hatcher, J.M., Kwiatkowski, N.P., Eser, P.O., Poitras, M.J., Wang, S., Xu, M., Gokhale, P.C., Cameron, M.D., Eck, M.J., Gray, N.S., Janne, P.A.

(2022) Cancer Res 82: 1633-1645

PubMed: 35149586 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1158/0008-5472.CAN-21-2693
Primary Citation Related Structures:
7JXH

PubMed Abstract:
In-frame insertions in exon 20 of HER2 are the most common HER2 mutations in patients with non-small cell lung cancer (NSCLC), a disease in which approved EGFR/HER2 tyrosine kinase inhibitors (TKI) display poor efficiency and undesirable side effects due to their strong inhibition of wild-type (WT) EGFR. Here, we report a HER2-selective covalent TKI, JBJ-08-178-01, that targets multiple HER2 activating mutations, including exon 20 insertions as well as amplification. JBJ-08-178-01 displayed strong selectivity toward HER2 mutants over WT EGFR compared with other EGFR/HER2 TKIs. Determination of the crystal structure of HER2 in complex with JBJ-08-178-01 suggests that an interaction between the inhibitor and Ser783 may be responsible for HER2 selectivity. The compound showed strong antitumoral activity in HER2-mutant or amplified cancers in vitro and in vivo. Treatment with JBJ-08-178-01 also led to a reduction in total HER2 by promoting proteasomal degradation of the receptor. Taken together, the dual activity of JBJ-08-178-01 as a selective inhibitor and destabilizer of HER2 represents a combination that may lead to better efficacy and tolerance in patients with NSCLC harboring HER2 genetic alterations or amplification. This study describes unique mechanisms of action of a new mutant-selective HER2 kinase inhibitor that reduces both kinase activity and protein levels of HER2 in lung cancer.

Organizational Affiliation

Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.

Macromolecule Content

Total Structure Weight: 299.58 kDa
Atom Count: 17,908
Modeled Residue Count: 2,190
Deposited Residue Count: 2,608
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	A [auth B] B [auth A] C D E A [auth B], B [auth A], C, D, E, F, G, H	326	Homo sapiens	Mutation(s): 0 Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626 Go to UniProtKB: P04626
PHAROS: P04626 GTEx: ENSG00000141736
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04626
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VOY (Subject of Investigation/LOI) Query on VOY Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth A] SDF format, chain I [auth B] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth B] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth B]	I [auth B] J [auth A] K [auth C] L [auth D] M [auth E] I [auth B], J [auth A], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	(2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide C₃₁ H₃₀ N₈ O₃ XBWYQGMQBNVPMF-VOTSOKGWSA-N		Interactions Focus chain I [auth B] Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth B] Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.27 Å
R-Value Free: 0.285 (Depositor), 0.285 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.138	α = 90
b = 154.617	β = 102.47
c = 93.548	γ = 90

Software Package:

Software Name	Purpose
xia2	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

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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