9QXN | pdb_00009qxn

Crystal Structure of wild-type EGFR in complex with the reversible inhibitor Sevabertinib (BAY 2927088)

PDB DOI: https://doi.org/10.2210/pdb9QXN/pdb

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

Deposited: 2025-04-16 Released: 2025-10-15
Deposition Author(s): Hillig, R.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.210 (Depositor), 0.218 (DCC)
R-Value Work:
0.156 (Depositor), 0.165 (DCC)

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

Sevabertinib, a Reversible HER2 Inhibitor with Activity in Lung Cancer.

Siegel, F., Siegel, S., Kotynkova, K., Karsli Uzunbas, G., Korr, D., Tomono, H., Andersen, S., Denney, D., Berger, M., Schulze, V.K., Lewis, T.A., Kaplan, B., Golfier, S., Mortier, J., Hillig, R.C., Boemer, U., Petersen, K., Eis, K., Williams, S., Ruttinger, D., Cherniack, A.D., Loong, H.H., Goto, K., Grassi, P., Meyerson, M., Greulich, H.

(2026) Cancer Discov 16: 81-94

PubMed: 41090369 Search on PubMed
DOI: https://doi.org/10.1158/2159-8290.CD-25-0605
Primary Citation Related Structures:
9QXN

PubMed Abstract:
Exon 20 insertions of HER2, encoded by ERBB2, and other activating HER2 mutations occur in 2-4% of lung adenocarcinomas, but there are only limited therapeutic options available for these patients. Sevabertinib (BAY 2927088) is a potent and reversible dual EGFR-HER2 inhibitor that is selective with respect to wild-type EGFR. Here, we report the preclinical activity of sevabertinib in lung cancer models harboring alterations of HER2, including exon 20 insertions, point mutations, and amplification of wild-type ERBB2. We furthermore demonstrate the activity of sevabertinib in a cancer cell line dependent on a fusion of NRG1, a ligand for the HER2 family member and heterodimerization partner, HER3. Finally, we report patient responses to sevabertinib from a Phase 1/2 clinical trial, indicating potential benefit for patients with HER2-mutant lung cancer.

Organizational Affiliation

Bayer AG, Germany.

Macromolecule Content

Total Structure Weight: 40.55 kDa
Atom Count: 3,162
Modeled Residue Count: 324
Deposited Residue Count: 346
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 AAA]	346	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JBI (Subject of Investigation/LOI) Query on A1JBI Download:Ideal Coordinates CCD File SDF format, chain H [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain H [auth AAA]	H [auth AAA]	3-[(3-chloranyl-2-methoxy-phenyl)amino]-2-[3-[[(2~{S})-1,4-dioxan-2-yl]methoxy]pyridin-4-yl]-1,5,6,7-tetrahydropyrrolo[3,2-c]pyridin-4-one C₂₄ H₂₅ Cl N₄ O₅ VYQVHWNNPKOJEA-AWEZNQCLSA-N		Interactions Focus chain H [auth AAA] Interactions & Density Focus chain H [auth AAA]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain B [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA], C [auth AAA]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA], G [auth AAA]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain G [auth AAA] Interactions & Density Focus chain E [auth AAA] Focus chain G [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Interactions & Density Focus chain F [auth AAA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth AAA] Interactions & Density Focus chain D [auth AAA]