4EZ3

CDK2 in complex with NSC 134199


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Novel Approach to the Discovery of Small-Molecule Ligands of CDK2.

Martin, M.P.Alam, R.Betzi, S.Ingles, D.J.Zhu, J.Y.Schonbrunn, E.

(2012) Chembiochem 13: 2128-2136

  • DOI: 10.1002/cbic.201200316
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In an attempt to identify novel small-molecule ligands of cyclin-dependent kinase 2 (CDK2) with potential as allosteric inhibitors, we have devised a robust and cost-effective fluorescence-based high-throughput screening assay. The assay is based on ...

    In an attempt to identify novel small-molecule ligands of cyclin-dependent kinase 2 (CDK2) with potential as allosteric inhibitors, we have devised a robust and cost-effective fluorescence-based high-throughput screening assay. The assay is based on the specific interaction of CDK2 with the extrinsic fluorophore 8-anilino-1-naphthalene sulfonate (ANS), which binds to a large allosteric pocket adjacent to the ATP site. Hit compounds that displace ANS directly or indirectly from CDK2 are readily classified as ATP site binders or allosteric ligands through the use of staurosporine, which blocks the ATP site without displacing ANS. Pilot screening of 1453 compounds led to the discovery of 12 compounds with displacement activities (EC(50) values) ranging from 6 to 44 μM, all of which were classified as ATP-site-directed ligands. Four new type I inhibitor scaffolds were confirmed by X-ray crystallography. Although this small compound library contained only ATP-site-directed ligands, the application of this assay to large compound libraries has the potential to reveal previously unrecognized chemical scaffolds suitable for structure-based design of CDK2 inhibitors with new mechanisms of action.


    Organizational Affiliation

    Drug Discovery Department, Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
306Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0S0
Query on 0S0

Download CCD File 
A
4-[(E)-(6-hydroxy-2-oxo-1,2-dihydropyridin-3-yl)diazenyl]benzenesulfonamide
C11 H10 N4 O4 S
NVVKOBSVOCFOEN-CCEZHUSRSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0S0IC50 :  45000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.42α = 90
b = 70.39β = 90
c = 71.46γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references