Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 

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This is version 1.3 of the entry. See complete history


6-Amino-3-methylpyrimidinones as Potent, Selective, and Orally Efficacious SHP2 Inhibitors.

Sarver, P.Acker, M.Bagdanoff, J.T.Chen, Z.Chen, Y.N.Chan, H.Firestone, B.Fodor, M.Fortanet, J.Hao, H.Hentemann, M.Kato, M.Koenig, R.LaBonte, L.R.Liu, G.Liu, S.Liu, C.McNeill, E.Mohseni, M.Sendzik, M.Stams, T.Spence, S.Tamez, V.Tichkule, R.Towler, C.Wang, H.Wang, P.Williams, S.L.Yu, B.LaMarche, M.J.

(2019) J Med Chem 62: 1793-1802

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01726
  • Primary Citation of Related Structures:  
    6MD7, 6MDB

  • PubMed Abstract: 

    Protein tyrosine phosphatase SHP2 is an oncoprotein associated with cancer as well as a potential immune modulator because of its role in the programmed cell death PD-L1/PD-1 pathway. In the preceding manuscript, we described the optimization of a fused, bicyclic screening hit for potency, selectivity, and physicochemical properties in order to further expand the chemical diversity of allosteric SHP2 inhibitors. In this manuscript, we describe the further expansion of our approach, morphing the fused, bicyclic system into a novel monocyclic pyrimidinone scaffold through our understanding of SAR and use of structure-based design. These studies led to the identification of SHP394 (1), an orally efficacious inhibitor of SHP2, with high lipophilic efficiency, improved potency, and enhanced pharmacokinetic properties. We also report other pyrimidinone analogues with favorable pharmacokinetic and potency profiles. Overall, this work improves upon our previously described allosteric inhibitors and exemplifies and extends the range of permissible chemical templates that inhibit SHP2 via the allosteric mechanism.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11
A, B
526Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JE1 (Subject of Investigation/LOI)
Query on JE1

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
C17 H20 F3 N5 O S
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
O4 P
Binding Affinity Annotations 
IDSourceBinding Affinity
JE1 BindingDB:  6MD7 IC50: 181 (nM) from 1 assay(s)
Binding MOAD:  6MD7 IC50: 181 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.05α = 90
b = 213.59β = 96.51
c = 55.91γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
autoPROCdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description