Crystal structure of non-receptor protein tyrosine phosphatase SHP2 in complex with inhibitor compound 24

Experimental Data Snapshot

  • Resolution: 2.06 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


Discovery of 5-Azaquinoxaline Derivatives as Potent and Orally Bioavailable Allosteric SHP2 Inhibitors.

Elsayed, M.S.A.Blake, J.F.Boys, M.L.Brown, E.Chapsal, B.D.Chicarelli, M.J.Cook, A.W.Fell, J.B.Fischer, J.P.Hanson, L.Lemieux, C.Martinson, M.C.McCown, J.McNulty, O.T.Mejia, M.J.Neitzel, N.A.Otten, J.N.Rodriguez, M.E.Wilcox, D.Wong, C.E.Zhou, Y.Hinklin, R.J.

(2023) ACS Med Chem Lett 14: 1673-1681

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00310
  • Primary Citation of Related Structures:  
    8U7W, 8U7X

  • PubMed Abstract: 

    SHP2 has emerged as an important target for oncology small-molecule drug discovery. As a nonreceptor tyrosine phosphatase within the MAPK pathway, it has been shown to control cell growth, differentiation, and oncogenic transformation. We used structure-based design to find a novel class of potent and orally bioavailable SHP2 inhibitors. Our efforts led to the discovery of the 5-azaquinoxaline as a new core for developing this class of compounds. Optimization of the potency and properties of this scaffold generated compound 30 , that exhibited potent in vitro SHP2 inhibition and showed excellent in vivo efficacy and pharmacokinetic profile.

  • Organizational Affiliation

    Medicinal Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11
A, B
539Homo sapiensMutation(s): 0 
Gene Names: PTPN11
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens)
Explore Q06124 
Go to UniProtKB:  Q06124
GTEx:  ENSG00000179295 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06124
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WAB (Subject of Investigation/LOI)
Query on WAB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C21 H24 Cl N7 O S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.06 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.44α = 90
b = 213.2β = 96.36
c = 55.77γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2024-01-03 
  • Deposition Author(s): Mou, T.C.

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release