Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844

Experimental Data Snapshot

  • Resolution: 2.09 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Dual Allosteric Inhibition of SHP2 Phosphatase.

Fodor, M.Price, E.Wang, P.Lu, H.Argintaru, A.Chen, Z.Glick, M.Hao, H.X.Kato, M.Koenig, R.LaRochelle, J.R.Liu, G.McNeill, E.Majumdar, D.Nishiguchi, G.A.Perez, L.B.Paris, G.Quinn, C.M.Ramsey, T.Sendzik, M.Shultz, M.D.Williams, S.L.Stams, T.Blacklow, S.C.Acker, M.G.LaMarche, M.J.

(2018) ACS Chem Biol 13: 647-656

  • DOI: https://doi.org/10.1021/acschembio.7b00980
  • Primary Citation of Related Structures:  
    6BMR, 6BMU, 6BMV, 6BMW, 6BMX, 6BMY

  • PubMed Abstract: 

    SHP2 is a cytoplasmic protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell proliferation, differentiation, and survival. Recently, we reported an allosteric mechanism of inhibition that stabilizes the auto-inhibited conformation of SHP2. SHP099 (1) was identified and characterized as a moderately potent, orally bioavailable, allosteric small molecule inhibitor, which binds to a tunnel-like pocket formed by the confluence of three domains of SHP2. In this report, we describe further screening strategies that enabled the identification of a second, distinct small molecule allosteric site. SHP244 (2) was identified as a weak inhibitor of SHP2 with modest thermal stabilization of the enzyme. X-ray crystallography revealed that 2 binds and stabilizes the inactive, closed conformation of SHP2, at a distinct, previously unexplored binding site-a cleft formed at the interface of the N-terminal SH2 and PTP domains. Derivatization of 2 using structure-based design resulted in an increase in SHP2 thermal stabilization, biochemical inhibition, and subsequent MAPK pathway modulation. Downregulation of DUSP6 mRNA, a downstream MAPK pathway marker, was observed in KYSE-520 cancer cells. Remarkably, simultaneous occupation of both allosteric sites by 1 and 2 was possible, as characterized by cooperative biochemical inhibition experiments and X-ray crystallography. Combining an allosteric site 1 inhibitor with an allosteric site 2 inhibitor led to enhanced pharmacological pathway inhibition in cells. This work illustrates a rare example of dual allosteric targeted protein inhibition, demonstrates screening methodology and tactics to identify allosteric inhibitors, and enables further interrogation of SHP2 in cancer and related pathologies.

  • Organizational Affiliation

    Novartis Institutes for Biomedical Research , Cambridge , Massachusetts 02139 , United States.

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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens)
Explore Q06124 
Go to UniProtKB:  Q06124
PHAROS:  Q06124
GTEx:  ENSG00000179295 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06124
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DYV (Subject of Investigation/LOI)
Query on DYV

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
C29 H24 Cl N5 O6
5OD (Subject of Investigation/LOI)
Query on 5OD

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
C16 H19 Cl2 N5
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
I [auth B],
J [auth B]
O4 P
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
5OD BindingDB:  6BMY IC50: min: 60, max: 84 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.09 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.05α = 90
b = 213.71β = 96.71
c = 55.98γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
autoPROCdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description