Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Compound 24

Experimental Data Snapshot

  • Resolution: 1.92 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 

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Identification of TNO155, an Allosteric SHP2 Inhibitor for the Treatment of Cancer.

LaMarche, M.J.Acker, M.Argintaru, A.Bauer, D.Boisclair, J.Chan, H.Chen, C.H.Chen, Y.N.Chen, Z.Deng, Z.Dore, M.Dunstan, D.Fan, J.Fekkes, P.Firestone, B.Fodor, M.Garcia-Fortanet, J.Fortin, P.D.Fridrich, C.Giraldes, J.Glick, M.Grunenfelder, D.Hao, H.X.Hentemann, M.Ho, S.Jouk, A.Kang, Z.B.Karki, R.Kato, M.Keen, N.Koenig, R.LaBonte, L.R.Larrow, J.Liu, G.Liu, S.Majumdar, D.Mathieu, S.Meyer, M.J.Mohseni, M.Ntaganda, R.Palermo, M.Perez, L.Pu, M.Ramsey, T.Reilly, J.Sarver, P.Sellers, W.R.Sendzik, M.Shultz, M.D.Slisz, J.Slocum, K.Smith, T.Spence, S.Stams, T.Straub, C.Tamez Jr., V.Toure, B.B.Towler, C.Wang, P.Wang, H.Williams, S.L.Yang, F.Yu, B.Zhang, J.H.Zhu, S.

(2020) J Med Chem 63: 13578-13594

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01170
  • Primary Citation of Related Structures:  
    7JVM, 7JVN

  • PubMed Abstract: 

    SHP2 is a nonreceptor protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also plays an important role in the programed cell death pathway (PD-1/PD-L1). As an oncoprotein as well as a potential immunomodulator, controlling SHP2 activity is of high therapeutic interest. As part of our comprehensive program targeting SHP2, we identified multiple allosteric binding modes of inhibition and optimized numerous chemical scaffolds in parallel. In this drug annotation report, we detail the identification and optimization of the pyrazine class of allosteric SHP2 inhibitors. Structure and property based drug design enabled the identification of protein-ligand interactions, potent cellular inhibition, control of physicochemical, pharmaceutical and selectivity properties, and potent in vivo antitumor activity. These studies culminated in the discovery of TNO155, (3 S ,4 S )-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)thio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine ( 1 ), a highly potent, selective, orally efficacious, and first-in-class SHP2 inhibitor currently in clinical trials for cancer.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11
A, B
525Homo sapiensMutation(s): 0 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VKP (Subject of Investigation/LOI)
Query on VKP

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
C16 H19 Cl2 N5 S
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B]
O4 P
Binding Affinity Annotations 
IDSourceBinding Affinity
VKP Binding MOAD:  7JVN IC50: 29 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.92 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.09α = 90
b = 214.736β = 97.09
c = 55.84γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description