8U7X

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

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.


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
539Homo sapiensMutation(s): 0 
Gene Names: PTPN11
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
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]
(3S,4S)-8-{6-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrido[2,3-b]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine
C21 H24 Cl N7 O S
CNWPAKCFVFDYQN-KPZWWZAWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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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