4RDD

Co-crystal structure of SHP2 in complex with a Cefsulodin derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Exploring the Existing Drug Space for Novel pTyr Mimetic and SHP2 Inhibitors.

He, R.Yu, Z.H.Zhang, R.Y.Wu, L.Gunawan, A.M.Lane, B.S.Shim, J.S.Zeng, L.F.He, Y.Chen, L.Wells, C.D.Liu, J.O.Zhang, Z.Y.

(2015) ACS Med Chem Lett 6: 782-786

  • DOI: https://doi.org/10.1021/acsmedchemlett.5b00118
  • Primary Citation of Related Structures:  
    4RDD

  • PubMed Abstract: 

    Protein tyrosine phosphatases (PTPs) are potential therapeutic targets for many diseases. Unfortunately, despite considerable drug discovery efforts devoted to PTPs, obtaining selective and cell permeable PTP inhibitors remains highly challenging. We describe a strategy to explore the existing drug space for previously unknown PTP inhibitory activities. This led to the discovery of cefsulodin as an inhibitor of SHP2, an oncogenic phosphatase in the PTP family. Crystal structure analysis of SHP2 interaction with cefsulodin identified sulfophenyl acetic amide (SPAA) as a novel phosphotyrosine (pTyr) mimetic. A structure-guided and SPAA fragment-based focused library approach produced several potent and selective SHP2 inhibitors. Notably, these inhibitors blocked SHP2-mediated signaling events and proliferation in several cancer cell lines. Thus, SPAA may serve as a new platform for developing chemical probes for other PTPs.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology and Chemical Genomics Core Facility, Indiana University School of Medicine , 635 Barnhill Drive, Indianapolis, Indiana 46202, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11275Homo 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
3LU
Query on 3LU

Download Ideal Coordinates CCD File 
B [auth A]1-({(2R)-4-carboxy-2-[(R)-carboxy{[(2R)-2-phenyl-2-sulfoacetyl]amino}methyl]-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyr idinium
C21 H22 N3 O8 S2
UZIDEBFKNVWIPU-YQVWRLOYSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
3LU Binding MOAD:  4RDD IC50: 1.68e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.638α = 90
b = 75.274β = 99.11
c = 48.046γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references