6OP9

HER3 pseudokinase domain bound to bosutinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Targetable HER3 functions driving tumorigenic signaling in HER2-amplified cancers.

Campbell, M.R.Ruiz-Saenz, A.Peterson, E.Agnew, C.Ayaz, P.Garfinkle, S.Littlefield, P.Steri, V.Oeffinger, J.Sampang, M.Shan, Y.Shaw, D.E.Jura, N.Moasser, M.M.

(2022) Cell Rep 38: 110291-110291

  • DOI: https://doi.org/10.1016/j.celrep.2021.110291
  • Primary Citation of Related Structures:  
    6OP9

  • PubMed Abstract: 

    Effective inactivation of the HER2-HER3 tumor driver has remained elusive because of the challenging attributes of the pseudokinase HER3. We report a structure-function study of constitutive HER2-HER3 signaling to identify opportunities for targeting. The allosteric activation of the HER2 kinase domain (KD) by the HER3 KD is required for tumorigenic signaling and can potentially be targeted by allosteric inhibitors. ATP binding within the catalytically inactive HER3 KD provides structural rigidity that is important for signaling, but this is mimicked, not opposed, by small molecule ATP analogs, reported here in a bosutinib-bound crystal structure. Mutational disruption of ATP binding and molecular dynamics simulation of the apo KD of HER3 identify a conformational coupling of the ATP pocket with a hydrophobic AP-2 pocket, analogous to EGFR, that is critical for tumorigenic signaling and feasible for targeting. The value of these potential target sites is confirmed in tumor growth assays using gene replacement techniques.


  • Organizational Affiliation

    Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-3328Homo sapiensMutation(s): 0 
Gene Names: ERBB3HER3
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21860 (Homo sapiens)
Explore P21860 
Go to UniProtKB:  P21860
PHAROS:  P21860
GTEx:  ENSG00000065361 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21860
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DB8 (Subject of Investigation/LOI)
Query on DB8

Download Ideal Coordinates CCD File 
B [auth A]4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile
C26 H29 Cl2 N5 O3
UBPYILGKFZZVDX-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DB8 BindingDB:  6OP9 Kd: 0.77 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.385α = 90
b = 116.385β = 90
c = 58.194γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States1BGIA744005

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection