1CKP

HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR PURVALANOL B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors.

Gray, N.S.Wodicka, L.Thunnissen, A.M.Norman, T.C.Kwon, S.Espinoza, F.H.Morgan, D.O.Barnes, G.LeClerc, S.Meijer, L.Kim, S.H.Lockhart, D.J.Schultz, P.G.

(1998) Science 281: 533-538


  • PubMed Abstract: 
  • Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent kinase 2 (CDK2). By iterating chemical library syn ...

    Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent kinase 2 (CDK2). By iterating chemical library synthesis and biological screening, potent inhibitors of the human CDK2-cyclin A kinase complex and of Saccharomyces cerevisiae Cdc28p were identified. The structural basis for the binding affinity and selectivity was determined by analysis of a three-dimensional crystal structure of a CDK2-inhibitor complex. The cellular effects of these compounds were characterized in mammalian cells and yeast. In the latter case the effects were characterized on a genome-wide scale by monitoring changes in messenger RNA levels in treated cells with high-density oligonucleotide probe arrays. Purine libraries could provide useful tools for analyzing a variety of signaling and regulatory pathways and may lead to the development of new therapeutics.


    Related Citations: 
    • Inhibition of Cyclin-Dependent Kinases by Purine Analogues-Crystal Structure of Human Cdk2 Complexed with Roscovitine
      De Azevedo, W.F.,Leclerc, S.,Meijer, L.,Havlicek, L.,Strnad, M.,Kim, S.H.
      (1997) Eur.J.Biochem. 243: 518
    • Crystal Structure of Cyclin-Dependent Kinase 2
      De Bondt, H.L.,Rosenblatt, J.,Jancarik, J.,Jones, H.D.,Morgan, D.O.,Kim, S.H.
      (1993) Nature 363: 595
    • Multiple Modes of Ligand Recognition: Crystal Structures of Cyclin-Dependent Protein Kinase 2 in Complex with ATP and Two Inhibitors, Olomoucine and Isopentenyladenine
      Schultze-Gahmen, U.,Brandsen, J.,Jones, H.D.,Morgan, D.O.,Meijer, L.,Vesely, J.,Kim, S.H.
      (1995) Protein Sci. 22: 378


    Organizational Affiliation

    Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CYCLIN-DEPENDENT PROTEIN KINASE 2)
A
298Homo sapiensGene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PVB
Query on PVB

Download SDF File 
Download CCD File 
A
PURVALANOL B
2-CHLORO-4-{[2-{[(1R)-1-(HYDROXYMETHYL)-2-METHYLPROPYL]AMINO}-9-(1-METHYLETHYL)-9H-PURIN-6-YL]AMINO}BENZOIC ACID
C20 H25 Cl N6 O3
ZKDXRFMOHZVXSG-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PVBIC50: 6 - 9 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.550α = 90.00
b = 71.350β = 90.00
c = 72.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
CCP4model building
DENZOdata reduction
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance