7VXG

Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TK-453


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

SHP2 allosteric inhibitor TK-453 alleviates psoriasis-like skin inflammation in mice via inhibition of IL-23/Th17 axis.

Wang, M.Li, T.Ouyang, Z.Tang, K.Zhu, Y.Song, C.Sun, H.Yu, B.Ji, X.Sun, Y.

(2022) iScience 25: 104009-104009

  • DOI: https://doi.org/10.1016/j.isci.2022.104009
  • Primary Citation of Related Structures:  
    7VXG

  • PubMed Abstract: 

    SHP2 is the first oncogenic tyrosine phosphatase encoded by PTPN11 , which plays a significant regulatory role in cancer and inflammation-related diseases. Although SHP2 allosteric inhibitors have been used in phase I/II clinical trials for solid tumors, whether SHP2 inhibition alleviates psoriasis remains unclear. Here we expressed and purified SHP2 related proteins, and established an enzyme activity screening system for different conformations of SHP2. We launched an iterative medicinal chemistry program and identified the lead compound, TK-453. Importantly, TK-453 possessed stronger affinity with SHP2 than SHP099, evidenced by the cocrystal structure of SHP2/TK-453, revealing that the additional aryl-S-aryl bridge in TK-453 induces a 1.8 Å shift of the dichlorophenyl ring and an approximate 20° deviation of the pyrazine ring plane relative to SHP099. Furthermore, TK-453 significantly ameliorated imiquimod-triggered skin inflammation in mice via inhibition of the IL-23/Th17 axis, proving that SHP2 is a potential therapeutic target for psoriasis.


  • Organizational Affiliation

    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China.


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, C, D
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.403α = 88.66
b = 55.596β = 102.01
c = 218.839γ = 96.19
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81872877
National Natural Science Foundation of China (NSFC)China91853109
National Natural Science Foundation of China (NSFC)China81773562

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description