7XHQ | pdb_00007xhq

Small-molecule Allosteric Regulation Mechanism of SHP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.275 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7XHQ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of the SHP2 allosteric inhibitor 2-((3R,4R)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl)-5-(2,3-dichlorophenyl)-3-methylpyrrolo[2,1-f][1,2,4] triazin-4(3H)-one.

Luo, Y.Li, J.Zong, Y.Sun, M.Zheng, W.Zhu, J.Liu, L.Liu, B.

(2023) J Enzyme Inhib Med Chem 38: 398-404

  • DOI: https://doi.org/10.1080/14756366.2022.2151594
  • Primary Citation Related Structures: 
    7XHQ

  • PubMed Abstract: 

    The non-receptor protein tyrosine phosphatase (PTP) SHP2 encoded by the PTPN11 gene is a critical regulator in a number of cellular signalling processes and pathways, including the MAPK and the immune-inhibitory programmed cell death PD-L1/PD-1 pathway. Hyperactivation and inactivation of SHP2 is of great therapeutic interest for its association with multiple developmental disorders and cancer-related diseases. In this work, we characterised a potent SHP2 allosteric inhibitor 2-((3 R,4R)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl)-5-(2,3-dichlorophenyl)-3-methylpyrrolo[2,1-f][1,2,4]triazin-4(3H)-one (PB17-026-01) by using structure-based design. To study the structure-activity relationship, we compared co-crystal structures of SHP2 bound with PB17-026-01 and its analogue compound PB17-036-01, which is ∼20-fold less active than PB17-026-01, revealing that both of the compounds are bound to SHP2 in the allosteric binding pocket and PB17-026-01 forms more polar contacts with its terminal group. Overall, our results provide new insights into the modes of action of allosteric SHP2 inhibitor and a guide for the design of SHP2 allosteric inhibitor.


  • Organizational Affiliation
    • School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.

Macromolecule Content 

  • Total Structure Weight: 121.42 kDa 
  • Atom Count: 7,664 
  • Modeled Residue Count: 946 
  • Deposited Residue Count: 1,050 
  • 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
525Homo sapiensMutation(s): 0 
Gene Names: SHPTP2
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
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FIZ

Query on FIZ



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2-[(3S,4R)-4-azanyl-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-5-[2,3-bis(chloranyl)phenyl]-3-methyl-pyrrolo[2,1-f][1,2,4]triazin-4-one
C22 H25 Cl2 N5 O2
CRDRKYXRTQUBHK-DJJJIMSYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.275 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.69α = 90
b = 91.39β = 90
c = 212.979γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
AUTOMARdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary