3H64

Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms complexed with endothall

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.195 

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:  
    3H69, 3H61, 3H62, 3H63, 3H64, 3H66, 3H67, 3H68, 3H60

  • 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 hydrolyzed w ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 5 A, D315Homo sapiensMutation(s): 0 
Gene Names: PPP5C, PPP5
EC: 3.1.3.16
Find proteins for P53041 (Homo sapiens)
Explore P53041 
Go to UniProtKB:  P53041
NIH Common Fund Data Resources
PHAROS:  P53041
GTEx:  ENSG00000011485
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ENL
Query on ENL
Download Ideal Coordinates CCD File 
A, D
(1R,2S,3R,4S)-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid
C8 H10 O5
GXEKYRXVRROBEV-FBXFSONDSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
A, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.553α = 90
b = 41.463β = 96.78
c = 95.614γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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