6MDC

Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyrimidinone 1 SHP389


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Optimization of Fused Bicyclic Allosteric SHP2 Inhibitors.

Bagdanoff, J.T.Chen, Z.Acker, M.Chen, Y.N.Chan, H.Dore, M.Firestone, B.Fodor, M.Fortanet, J.Hentemann, M.Kato, M.Koenig, R.LaBonte, L.R.Liu, S.Mohseni, M.Ntaganda, R.Sarver, P.Smith, T.Sendzik, M.Stams, T.Spence, S.Towler, C.Wang, H.Wang, P.Williams, S.L.LaMarche, M.J.

(2019) J Med Chem 62: 1781-1792

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01725
  • Primary Citation of Related Structures:  
    6MD9, 6MDA, 6MDC, 6MDD

  • PubMed Abstract: 

    SHP2 is a nonreceptor protein tyrosine phosphatase within the mitogen-activated protein kinase (MAPK) pathway controlling cell growth, differentiation, and oncogenic transformation. SHP2 also participates in the programed cell death pathway (PD-1/PD-L1) governing immune surveillance. Small-molecule inhibition of SHP2 has been widely investigated, including in our previous reports describing SHP099 (2), which binds to a tunnel-like allosteric binding site. To broaden our approach to allosteric inhibition of SHP2, we conducted additional hit finding, evaluation, and structure-based scaffold morphing. These studies, reported here in the first of two papers, led to the identification of multiple 5,6-fused bicyclic scaffolds that bind to the same allosteric tunnel as 2. We demonstrate the structural diversity permitted by the tunnel pharmacophore and culminated in the identification of pyrazolopyrimidinones (e.g., SHP389, 1) that modulate MAPK signaling in vivo. These studies also served as the basis for further scaffold morphing and optimization, detailed in the following manuscript.


  • Organizational Affiliation

    Chemical and Pharmaceutical Profiling , Novartis Pharmaceuticals , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11
A, B
526Homo sapiensMutation(s): 0 
Gene Names: PTPN11PTP2CSHPTP2
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens)
Explore Q06124 
Go to UniProtKB:  Q06124
GTEx:  ENSG00000179295 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06124
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
JEA Binding MOAD:  6MDC IC50: 36 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.49α = 90
b = 213.77β = 97.02
c = 56.3γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-25
    Changes: Data collection, Refinement description