6MDA

Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyridine 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.8b01725
  • Primary Citation of Related Structures:  

  • 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- ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 11
A, B
526Homo sapiensMutation(s): 0 
Gene Names: PTPN11 (PTP2C, SHPTP2)
EC: 3.1.3.48
Find proteins for Q06124 (Homo sapiens)
Go to Gene View: PTPN11
Go to UniProtKB:  Q06124
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JED
Query on JED

Download SDF File 
Download CCD File 
A, B
3-(4-bromophenyl)-6-(4-methylphenyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid
C20 H14 Br N3 O2
ZSKVLMBZFPQPHV-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.630α = 90.00
b = 213.290β = 96.86
c = 56.000γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AutoPROCdata scaling
BUSTERrefinement
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-09-04 
  • Released Date: 2019-02-13 
  • Deposition Author(s): Fodor, M., Stams, T.

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references