9QXN | pdb_00009qxn

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


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 1.1 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.

(2025) Cancer Discov 

  • DOI: https://doi.org/10.1158/2159-8290.CD-25-0605
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epidermal growth factor receptorA [auth AAA]346Homo sapiensMutation(s): 0 
Gene Names: EGFRERBBERBB1HER1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00533
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JBI (Subject of Investigation/LOI)
Query on A1JBI

Download Ideal Coordinates CCD File 
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
SIN
Query on SIN

Download Ideal Coordinates CCD File 
B [auth AAA],
C [auth AAA]
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth AAA],
G [auth AAA]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth AAA]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.43α = 90
b = 147.43β = 90
c = 147.43γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-10-15 
  • Deposition Author(s): Hillig, R.C.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references