6CMS

Closed structure of active SHP2 mutant E76K bound to SHP099 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2.

Padua, R.A.P.Sun, Y.Marko, I.Pitsawong, W.Stiller, J.B.Otten, R.Kern, D.

(2018) Nat Commun 9: 4507-4507

  • DOI: 10.1038/s41467-018-06814-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein tyrosine phosphatase SHP2 functions as a key regulator of cell cycle control, and activating mutations cause several cancers. Here, we dissect the energy landscape of wild-type SHP2 and the oncogenic mutation E76K. NMR spectroscopy and X-ray ...

    Protein tyrosine phosphatase SHP2 functions as a key regulator of cell cycle control, and activating mutations cause several cancers. Here, we dissect the energy landscape of wild-type SHP2 and the oncogenic mutation E76K. NMR spectroscopy and X-ray crystallography reveal that wild-type SHP2 exchanges between closed, inactive and open, active conformations. E76K mutation shifts this equilibrium toward the open state. The previously unknown open conformation is characterized, including the active-site WPD loop in the inward and outward conformations. Binding of the allosteric inhibitor SHP099 to E76K mutant, despite much weaker, results in an identical structure as the wild-type complex. A conformational selection to the closed state reduces drug affinity which, combined with E76K's much higher activity, demands significantly greater SHP099 concentrations to restore wild-type  activity levels. The differences in structural ensembles and drug-binding kinetics of cancer-associated SHP2 forms may stimulate innovative ideas for developing more potent inhibitors for activated SHP2 mutants.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA, 02454, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 11
A
532Homo 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
5OD
Query on 5OD

Download SDF File 
Download CCD File 
A
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.205 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.715α = 90.00
b = 54.141β = 90.00
c = 218.847γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
PHENIXrefinement
Blu-Icedata collection
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological DevelopmentBrazil233809/2014-7
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM100966

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2019-04-17
    Type: Author supporting evidence, Data collection