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): 

  • 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: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.7b01520

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 11
A
557Homo sapiensMutation(s): 1 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8J6
Query on 8J6

Download SDF File 
Download CCD File 
A
4-(3-phenylphenyl)-N-(2,2,6,6-tetramethylpiperidin-4-yl)-1,3-thiazol-2-amine
C24 H29 N3 S
SFPHCJXSQMJICI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.280α = 90.00
b = 55.750β = 90.00
c = 219.190γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Database references