5EHR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/nature18621
  • Primary Citation of Related Structures:  
    5EHR

  • 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 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:  (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
PHAROS:  Q06124
GTEx:  ENSG00000179295 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06124
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5OD
Query on 5OD

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine
C16 H19 Cl2 N5
YGUFCDOEKKVKJK-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Binding Affinity Annotations 
IDSourceBinding Affinity
5OD BindingDB:  5EHR Ki: 67 (nM) from 1 assay(s)
Kd: min: 73, max: 1500 (nM) from 2 assay(s)
IC50: min: 0.14, max: 250 (nM) from 10 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.19α = 90
b = 213.79β = 96.88
c = 55.89γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description