2YDU

Crystal structure of YopH in complex with 3-(1,1-dioxido-3- oxoisothiazolidin-5-yl)benzaldeyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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This is version 1.1 of the entry. See complete history


Literature

Isothiazolidinone (Izd) as a Phosphoryl Mimetic in Inhibitors of the Yersinia Pestis Protein Tyrosine Phosphatase Yoph.

Kim, S.E.Bahta, M.Lountos, G.T.Ulrich, R.G.Burke, T.R.Waugh, D.S.

(2011) Acta Crystallogr D Biol Crystallogr 67: 639

  • DOI: https://doi.org/10.1107/S0907444911018610
  • Primary Citation of Related Structures:  
    2YDU

  • PubMed Abstract: 

    Isothiazolidinone (IZD) heterocycles can act as effective components of protein tyrosine phosphatase (PTP) inhibitors by simultaneously replicating the binding interactions of both a phosphoryl group and a highly conserved water molecule, as exemplified by the structures of several PTP1B-inhibitor complexes. In the first unambiguous demonstration of IZD interactions with a PTP other than PTP1B, it is shown by X-ray crystallography that the IZD motif binds within the catalytic site of the Yersinia pestis PTP YopH by similarly displacing a highly conserved water molecule. It is also shown that IZD-based bidentate ligands can inhibit YopH in a nonpromiscuous fashion at low micromolar concentrations. Hence, the IZD moiety may represent a useful starting point for the development of YopH inhibitors.


  • Organizational Affiliation

    Chemical Biology Laboratory, National Cancer Institute at Frederick, MD 21702-1201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OUTER PROTEIN H PHOSPHATASE306Yersinia pestisMutation(s): 0 
UniProt
Find proteins for O68720 (Yersinia pestis)
Explore O68720 
Go to UniProtKB:  O68720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68720
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
79W
Query on 79W

Download Ideal Coordinates CCD File 
B [auth A]3-[(2S)-1,1-DIOXIDO-4-OXOTETRAHYDROTHIOPHEN-2-YL]BENZALDEHYDE
C11 H10 O4 S
YIJQNPNARRVHGF-NSHDSACASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.307α = 90
b = 55.912β = 90
c = 99.055γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description