5EHR

Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP099


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases.

Chen, Y.P.LaMarche, M.J.Chan, H.M.Fekkes, P.Garcia-Fortanet, J.Acker, M.G.Antonakos, B.Chen, C.H.Chen, Z.Cooke, V.G.Dobson, J.R.Deng, Z.Fei, F.Firestone, B.Fodor, M.Fridrich, C.Gao, H.Grunenfelder, D.Hao, H.X.Jacob, J.Ho, S.Hsiao, K.Kang, Z.B.Karki, R.Kato, M.Larrow, J.La Bonte, L.R.Lenoir, F.Liu, G.Liu, S.Majumdar, D.Meyer, M.J.Palermo, M.Perez, L.Pu, M.Price, E.Quinn, C.Shakya, S.Shultz, M.D.Slisz, J.Venkatesan, K.Wang, P.Warmuth, M.Williams, S.Yang, G.Yuan, J.Zhang, J.H.Zhu, P.Ramsey, T.Keen, N.J.Sellers, W.R.Stams, T.Fortin, P.D.

(2016) Nature 535: 148-152

  • DOI: 10.1038/nature18621

  • PubMed Abstract: 
  • The non-receptor protein tyrosine phosphatase SHP2, encoded by PTPN11, has an important role in signal transduction downstream of growth factor receptor signalling and was the first reported oncogenic tyrosine phosphatase. Activating mutations of SHP ...

    The non-receptor protein tyrosine phosphatase SHP2, encoded by PTPN11, has an important role in signal transduction downstream of growth factor receptor signalling and was the first reported oncogenic tyrosine phosphatase. Activating mutations of SHP2 have been associated with developmental pathologies such as Noonan syndrome and are found in multiple cancer types, including leukaemia, lung and breast cancer and neuroblastoma. SHP2 is ubiquitously expressed and regulates cell survival and proliferation primarily through activation of the RAS–ERK signalling pathway. It is also a key mediator of the programmed cell death 1 (PD-1) and B- and T-lymphocyte attenuator (BTLA) immune checkpoint pathways. Reduction of SHP2 activity suppresses tumour cell growth and is a potential target of cancer therapy. Here we report the discovery of a highly potent (IC50 = 0.071 μM), selective and orally bioavailable small-molecule SHP2 inhibitor, SHP099, that stabilizes SHP2 in an auto-inhibited conformation. SHP099 concurrently binds to the interface of the N-terminal SH2, C-terminal SH2, and protein tyrosine phosphatase domains, thus inhibiting SHP2 activity through an allosteric mechanism. SHP099 suppresses RAS–ERK signalling to inhibit the proliferation of receptor-tyrosine-kinase-driven human cancer cells in vitro and is efficacious in mouse tumour xenograft models. Together, these data demonstrate that pharmacological inhibition of SHP2 is a valid therapeutic approach for the treatment of cancers.



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
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
5OD
Query on 5OD

Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5ODKd: 73 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.190α = 90.00
b = 213.790β = 96.88
c = 55.890γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-10-28 
  • Released Date: 2016-06-29 
  • Deposition Author(s): Stams, T., Fodor, M.

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-13
    Type: Database references
  • Version 1.2: 2016-07-20
    Type: Database references