5XZR

The atomic structure of SHP2 E76A mutant in complex with allosteric inhibitor 9b

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2017-07-13 Released: 2017-12-13 
  • Deposition Author(s): Li, D., Xie, J., Zhu, J., Liu, C.
  • Funding Organization(s): The 100 Talents Program of Chinese Academy of Sciences, The Personalized Medicines-Molecular Signature-based Drug Discovery and Development Strategic Priority Research Program of the Chinese Academy of Sciences, Shanghai Municipal Committee of Science and Technology, A State High-Tech Development Plan (the 863 Program) Award, The National Key Research and Development Program

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Allosteric Inhibitors of SHP2 with Therapeutic Potential for Cancer Treatment.

Xie, J.Si, X.Gu, S.Wang, M.Shen, J.Li, H.Shen, J.Li, D.Fang, Y.Liu, C.Zhu, J.

(2017) J Med Chem 60: 10205-10219

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01520
  • Primary Citation of Related Structures:  
    5XZR

  • PubMed Abstract: 

    SHP2, a cytoplasmic protein-tyrosine phosphatase encoded by the PTPN11 gene, is involved in multiple cell signaling processes including Ras/MAPK and Hippo/YAP pathways. SHP2 has been shown to contribute to the progression of a number of cancer types including leukemia, gastric, and breast cancers. It also regulates T-cell activation by interacting with inhibitory immune checkpoint receptors such as the programmed cell death 1 (PD-1) and B- and T-lymphocyte attenuator (BTLA). Thus, SHP2 inhibitors have drawn great attention by both inhibiting tumor cell proliferation and activating T cell immune responses toward cancer cells. In this study, we report the identification of an allosteric SHP2 inhibitor 1-(4-(6-bromonaphthalen-2-yl)thiazol-2-yl)-4-methylpiperidin-4-amine (23) that locks SHP2 in a closed conformation by binding to the interface of the N-terminal SH2, C-terminal SH2, and phosphatase domains. Compound 23 suppresses MAPK signaling pathway and YAP transcriptional activity and shows antitumor activity in vivo. The results indicate that allosteric inhibition of SHP2 could be a feasible approach for cancer therapy.


  • Organizational Affiliation

    Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 26 Qiuyue Road, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11557Homo sapiensMutation(s): 1 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8J6
Query on 8J6

Download Ideal Coordinates CCD File 
B [auth A]4-(3-phenylphenyl)-N-(2,2,6,6-tetramethylpiperidin-4-yl)-1,3-thiazol-2-amine
C24 H29 N3 S
SFPHCJXSQMJICI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.28α = 90
b = 55.75β = 90
c = 219.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The 100 Talents Program of Chinese Academy of SciencesChina--
The Personalized Medicines-Molecular Signature-based Drug Discovery and Development Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDA12000000
Shanghai Municipal Committee of Science and TechnologyChina14ZR1448600, 15ZR1449000
A State High-Tech Development Plan (the 863 Program) AwardChina2015AA020907
The National Key Research and Development ProgramChina2016YFA0501900

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description