Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.20 kDa 
• Atom Count: 1873 
• Modelled Residue Count: 177 
• Deposited Residue Count: 183 
• Unique protein chains: 1

4WH9

Structure of the CDC25B Phosphatase Catalytic Domain with Bound Inhibitor

• PDB DOI: 10.2210/pdb4WH9/pdb

• Classification: HYDROLASE/HYDROLASE Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-09-20 Released: 2014-12-10 
• Deposition Author(s): Lund, G.L., Dudkin, S., Borkin, D., Ni, W., Grembecka, J., Cierpicki, T.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.152 
• R-Value Work: 0.126 
• R-Value Observed: 0.127 

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

• PubMed: 25423142 
• DOI: 10.1021/cb500883h
• Primary Citation of Related Structures:  
  4WH7, 4WH9


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M-phase inducer phosphatase 2	A	183	Homo sapiens	Mutation(s): 1  Gene Names: CDC25B, CDC25HU2 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P30305 (Homo sapiens) Explore P30305  Go to UniProtKB:  P30305
PHAROS:  P30305

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3M8	B [auth A]	2-[(2-cyano-3-fluoro-5-hydroxyphenyl)sulfanyl]ethanesulfonic acid C9 H8 F N O4 S2 ZFJOGPQOJAOGAK-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3M8	Binding MOAD:  4WH9	IC50: 2.20e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.152 
• R-Value Work: 0.126 
• R-Value Observed: 0.127 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.66	α = 90
b = 71.47	β = 90
c = 73.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-09-20 
• Released Date: 2014-12-10 
Deposition Author(s): Lund, G.L., Dudkin, S., Borkin, D., Ni, W., Grembecka, J., Cierpicki, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA181185

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2015-03-04
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence