7PCD

HER2 IN COMPLEX WITH A COVALENT INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of potent and selective HER2 inhibitors with efficacy against HER2 exon 20 insertion-driven tumors, which preserve wild-type EGFR signaling.

Wilding, B.Scharn, D.Bose, D.Baum, A.Santoro, V.Chetta, P.Schnitzer, R.Botesteanu, D.A.Reiser, C.Kornigg, S.Knesl, P.Hormann, A.Koferle, A.Corcokovic, M.Lieb, S.Scholz, G.Bruchhaus, J.Spina, M.Balla, J.Peric-Simov, B.Zimmer, J.Mitzner, S.Fett, T.N.Beran, A.Lamarre, L.Gerstberger, T.Gerlach, D.Bauer, M.Bergner, A.Schlattl, A.Bader, G.Treu, M.Engelhardt, H.Zahn, S.Fuchs, J.E.Zuber, J.Ettmayer, P.Pearson, M.Petronczki, M.Kraut, N.McConnell, D.B.Solca, F.Neumuller, R.A.

(2022) Nat Cancer 3: 821-836

  • DOI: https://doi.org/10.1038/s43018-022-00412-y
  • Primary Citation of Related Structures:  
    7PCD

  • PubMed Abstract: 

    Oncogenic alterations in human epidermal growth factor receptor 2 (HER2) occur in approximately 2% of patients with non-small cell lung cancer and predominantly affect the tyrosine kinase domain and cluster in exon 20 of the ERBB2 gene. Most clinical-grade tyrosine kinase inhibitors are limited by either insufficient selectivity against wild-type (WT) epidermal growth factor receptor (EGFR), which is a major cause of dose-limiting toxicity or by potency against HER2 exon 20 mutant variants. Here we report the discovery of covalent tyrosine kinase inhibitors that potently inhibit HER2 exon 20 mutants while sparing WT EGFR, which reduce tumor cell survival and proliferation in vitro and result in regressions in preclinical xenograft models of HER2 exon 20 mutant non-small cell lung cancer, concomitant with inhibition of downstream HER2 signaling. Our results suggest that HER2 exon 20 insertion-driven tumors can be effectively treated by a potent and highly selective HER2 inhibitor while sparing WT EGFR, paving the way for clinical translation.


  • Organizational Affiliation

    Boehringer Ingelheim RCV, Vienna, Austria. birgit.wilding@boehringer-ingelheim.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-2327Homo sapiensMutation(s): 0 
Gene Names: ERBB2HER2MLN19NEUNGL
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04626
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
70I (Subject of Investigation/LOI)
Query on 70I

Download Ideal Coordinates CCD File 
B [auth A]1-[4-[4-[[3,5-bis(chloranyl)-4-([1,2,4]triazolo[1,5-a]pyridin-7-yloxy)phenyl]amino]pyrimido[5,4-d]pyrimidin-6-yl]piperazin-1-yl]-4-(3-fluoranylazetidin-1-yl)butan-1-one
C29 H28 Cl2 F N11 O2
INUHBCAMHFOBPF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.009α = 90
b = 94.471β = 90
c = 80.325γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-07-27 
  • Deposition Author(s): Bader, G.

Funding OrganizationLocationGrant Number
Austrian Research Promotion AgencyAustria872827; 0879012

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary