6BMY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/acschembio.7b00980
  • Primary Citation of Related Structures:  

  • 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 conforma ...

    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.



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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5OD
Query on 5OD

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Download CCD File 
A, B
6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine
SHP099
C16 H19 Cl2 N5
YGUFCDOEKKVKJK-UHFFFAOYSA-N
 Ligand Interaction
DYV
Query on DYV

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Download CCD File 
A, B
1-(3-chloro-4-{[1-(2-hydroxy-3-methoxyphenyl)-5-oxo[1,2,4]triazolo[4,3-a]quinazolin-4(5H)-yl]methyl}benzene-1-carbonyl)-L-proline
C29 H24 Cl N5 O6
SUGSJIDJUCFQEX-QFIPXVFZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.050α = 90.00
b = 213.710β = 96.71
c = 55.980γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
AutoPROCdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-11-15 
  • Released Date: 2018-01-17 
  • Deposition Author(s): Stams, T., Fodor, M.

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Database references