3H63

Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms originally soaked with cantharidin (which is present in the structure in the hydrolyzed form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of serine/threonine phosphatase inhibition by the archetypal small molecules cantharidin and norcantharidin

Bertini, I.Calderone, V.Fragai, M.Luchinat, C.Talluri, E.

(2009) J.Med.Chem. 52: 4838-4843

  • DOI: 10.1021/jm900610k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The inhibition of a subgroup of human serine/threonine protein phosphatases is responsible for the cytotoxicity of cantharidin and norcantharidin against tumor cells. It is shown that the anhydride rings of cantharidin and norcantharidin are hydrolyz ...

    The inhibition of a subgroup of human serine/threonine protein phosphatases is responsible for the cytotoxicity of cantharidin and norcantharidin against tumor cells. It is shown that the anhydride rings of cantharidin and norcantharidin are hydrolyzed when bound to the catalytic domain of the human serine/threonine protein phosphatases 5 (PP5c), and the high-resolution crystal structures of PP5c complexed with the corresponding dicarboxylic acid derivatives of the two molecules are reported. Norcantharidin shows a unique binding conformation with the catalytically active Mn2PP5c, while cantharidin is characterized by a double conformation in its binding mode to the protein. Different binding modes of norcantharidin are observed depending of whether the starting ligand is in the anhydride or in the dicarboxylic acid form. All these structures will provide the basis for the rational design of new cantharidin-based drugs.


    Organizational Affiliation

    Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy. bertini@cerm.unifi.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 5
A, C
315Homo sapiensMutation(s): 0 
Gene Names: PPP5C (PPP5)
EC: 3.1.3.16
Find proteins for P53041 (Homo sapiens)
Go to Gene View: PPP5C
Go to UniProtKB:  P53041
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NHC
Query on NHC

Download SDF File 
Download CCD File 
A, C
(1R,2S,3R,4S)-2,3-dimethyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid
Cantharidic acid
C10 H14 O5
NMTNUQBORQILRK-XCVPVQRUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.464α = 90.00
b = 41.784β = 96.88
c = 105.833γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
ADSCdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance