4WH7

Structure of the CDC25B Phosphatase Catalytic Domain with Bound Ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibition of CDC25B Phosphatase Through Disruption of Protein-Protein Interaction.

Lund, G.Dudkin, S.Borkin, D.Ni, W.Grembecka, J.Cierpicki, T.

(2015) Acs Chem.Biol. 10: 390-394

  • DOI: 10.1021/cb500883h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CDC25 phosphatases are key cell cycle regulators and represent very attractive but challenging targets for anticancer drug discovery. Here, we explored whether fragment-based screening represents a valid approach to identify inhibitors of CDC25B. Thi ...

    CDC25 phosphatases are key cell cycle regulators and represent very attractive but challenging targets for anticancer drug discovery. Here, we explored whether fragment-based screening represents a valid approach to identify inhibitors of CDC25B. This resulted in identification of 2-fluoro-4-hydroxybenzonitrile, which directly binds to the catalytic domain of CDC25B. Interestingly, NMR data and the crystal structure demonstrate that this compound binds to the pocket distant from the active site and adjacent to the protein-protein interaction interface with CDK2/Cyclin A substrate. Furthermore, we developed a more potent analogue that disrupts CDC25B interaction with CDK2/Cyclin A and inhibits dephosphorylation of CDK2. Based on these studies, we provide a proof of concept that targeting CDC25 phosphatases by inhibiting their protein-protein interactions with CDK2/Cyclin A substrate represents a novel, viable opportunity to target this important class of enzymes.


    Organizational Affiliation

    Department of Pathology, University of Michigan , 4510C MSRBI 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-5620, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M-phase inducer phosphatase 2
A
183Homo sapiensMutation(s): 1 
Gene Names: CDC25B (CDC25HU2)
EC: 3.1.3.48
Find proteins for P30305 (Homo sapiens)
Go to Gene View: CDC25B
Go to UniProtKB:  P30305
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
8H8
Query on 8H8

Download SDF File 
Download CCD File 
A
2-fluoro-4-hydroxybenzonitrile
C7 H4 F N O
REIVHYDACHXPNH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8H8IC50: >5000000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.207α = 90.00
b = 71.442β = 90.00
c = 73.476γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
HKL-2000data reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA181185

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Derived calculations
  • Version 1.2: 2015-03-04
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Source and taxonomy