3F81

Interaction of VHR with SA3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Multidentate small-molecule inhibitors of vaccinia H1-related (VHR) phosphatase decrease proliferation of cervix cancer cells.

Wu, S.Vossius, S.Rahmouni, S.Miletic, A.V.Vang, T.Vazquez-Rodriguez, J.Cerignoli, F.Arimura, Y.Williams, S.Hayes, T.Moutschen, M.Vasile, S.Pellecchia, M.Mustelin, T.Tautz, L.

(2009) J Med Chem 52: 6716-6723

  • DOI: https://doi.org/10.1021/jm901016k
  • Primary Citation of Related Structures:  
    3F81

  • PubMed Abstract: 

    Loss of VHR phosphatase causes cell cycle arrest in HeLa carcinoma cells, suggesting that VHR inhibition may be a useful approach to halt the growth of cancer cells. We recently reported that VHR is upregulated in several cervix cancer cell lines as well as in carcinomas of the uterine cervix. Here we report the development of multidentate small-molecule inhibitors of VHR that inhibit its enzymatic activity at nanomolar concentrations and exhibit antiproliferative effects on cervix cancer cells. Chemical library screening was used to identify hit compounds, which were further prioritized in profiling and kinetic experiments. SAR analysis was applied in the search for analogs with improved potency and selectivity, resulting in the discovery of novel inhibitors that are able to interact with both the phosphate-binding pocket and several distinct hydrophobic regions within VHR's active site. This multidentate binding mode was confirmed by X-ray crystallography. The inhibitors decreased the proliferation of cervix cancer cells, while growth of primary normal keratinocytes was not affected. These compounds may be a starting point to develop drugs for the treatment of cervical cancer.


  • Organizational Affiliation

    Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, California 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity protein phosphatase 3
A, B
183Homo sapiensMutation(s): 0 
Gene Names: DUSP3VHR
EC: 3.1.3.48 (PDB Primary Data), 3.1.3.16 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P51452 (Homo sapiens)
Explore P51452 
Go to UniProtKB:  P51452
PHAROS:  P51452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51452
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
STT
Query on STT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-[(5~{E})-5-[[3-[4-(2-fluoranylphenoxy)phenyl]-1-phenyl-pyrazol-4-yl]methylidene]-4-oxidanylidene-2-sulfanylidene-1,3-thiazolidin-3-yl]ethanesulfonic acid
C27 H20 F N3 O5 S3
JNBMBOFCJMRUHR-LFVJCYFKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
STT PDBBind:  3F81 IC50: 74 (nM) from 1 assay(s)
Binding MOAD:  3F81 IC50: 74 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.406α = 90
b = 59.186β = 98.36
c = 60.656γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-02-19
    Changes: Advisory, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description