8U8X

crystal structure of the receptor tyrosine kinase Human HER2 (ERBB2) YVMA mutant kinase domain in complex with inhibitor compound 27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Potent and Selective Covalent Inhibitors of HER2 WT and HER2 YVMA .

Hicken, E.J.Brown, K.Dwulet, N.C.Gaudino, J.J.Hansen, E.P.Hartley, D.P.Kowalski, J.P.Laird, E.R.Lazzara, N.C.Li, B.Mou, T.C.Mutryn, M.F.Oko, L.Pajk, S.Pipal, R.W.Rosen, R.Z.Shelp, R.Singh, A.Wang, J.Wise, C.E.Wong, C.Wong, J.Y.

(2024) J Med Chem 67: 9759-9771

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00978
  • Primary Citation of Related Structures:  
    8U8X

  • PubMed Abstract: 

    HER2 overexpression and amplification have been identified as oncogenic drivers, and the development of therapies to treat tumors harboring these markers has received considerable attention. Activation of HER2 signaling and subsequent cell growth can also be induced by HER2 mutations, including the common YVMA insertion in exon 20 within the kinase domain. Enhertu is currently the only approved treatment for HER2 mutant tumors in NSCLC. TKIs tested in this space have suffered from off-target activity, primarily due to EGFR WT inhibition or attenuated activity against HER2 mutants. The goal of this work was to identify a TKI that would provide robust inhibition of oncogenic HER2 WT and HER2 mutants while sparing EGFR WT activity. Herein, we describe the development of a potent, covalent inhibitor of HER2 WT and the YVMA insertion mutant while providing oral bioavailability and avoiding the inhibition of EGFR WT .


  • Organizational Affiliation

    Pfizer Boulder Research and Development, Boulder, Colorado 80301, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-2348Homo sapiensMutation(s): 0 
Gene Names: ERBB2
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W9N (Subject of Investigation/LOI)
Query on W9N

Download Ideal Coordinates CCD File 
B [auth A]1-{(1R,3r,5S)-3-[(3M)-4-methyl-3-{3-methyl-4-[(1-methyl-1H-benzimidazol-5-yl)oxy]phenyl}-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-8-azabicyclo[3.2.1]octan-8-yl}propan-1-one
C31 H33 N7 O2
HOVNOYPBTGQGSF-JKHIJQBDSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.42α = 90
b = 59.42β = 90
c = 82.484γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references