8CBH | pdb_00008cbh

SHP2 in complex with a novel allosteric inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.264 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Novel Series of Imidazopyrazine Derivatives as Potent SHP2 Allosteric Inhibitors.

Torrente, E.Fodale, V.Ciammaichella, A.Ferrigno, F.Ontoria, J.M.Ponzi, S.Rossetti, I.Sferrazza, A.Amaudrut, J.Missineo, A.Esposito, S.Palombo, S.Nibbio, M.Cerretani, M.Bisbocci, M.Cellucci, A.di Marco, A.Alli, C.Pucci, V.Toniatti, C.Petrocchi, A.

(2023) ACS Med Chem Lett 14: 156-162

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00454
  • Primary Citation Related Structures: 
    8B5Y, 8CBH

  • PubMed Abstract: 

    Protein tyrosine phosphatase SHP2 is an oncogenic protein that can regulate different cytokine receptor and receptor tyrosine kinase signaling pathways. We report here the identification of a novel series of SHP2 allosteric inhibitors having an imidazopyrazine 6,5-fused heterocyclic system as the central scaffold that displays good potency in enzymatic and cellular assays. SAR studies led to the identification of compound 8 , a highly potent SHP2 allosteric inhibitor. X-ray studies showed novel stabilizing interactions with respect to known SHP2 inhibitors. Subsequent optimization allowed us to identify analogue 10 , which possesses excellent potency and a promising PK profile in rodents.


  • Organizational Affiliation
    • Department of Drug Discovery IRBM S.p.A., Pomezia, Rome 00071, Italy.

Macromolecule Content 

  • Total Structure Weight: 121.58 kDa 
  • Atom Count: 8,210 
  • Modeled Residue Count: 971 
  • Deposited Residue Count: 1,052 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11
A, B
526Homo sapiensMutation(s): 0 
Gene Names: PTPN11PTP2CSHPTP2
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
U70
(Subject of Investigation/LOI)

Query on U70



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
[(1~{S},6~{R},7~{S})-3-[3-[2,3-bis(chloranyl)phenyl]-2~{H}-pyrazolo[3,4-b]pyrazin-6-yl]-7-(4-methyl-1,3-thiazol-2-yl)-3-azabicyclo[4.1.0]heptan-7-yl]methanamine
C22 H21 Cl2 N7 S
BDJJZYXDJQVPIV-QLEMLULZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.264 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.888α = 90
b = 215.966β = 95.11
c = 55.829γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection