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 
  • R-Value Observed: 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

  • DOI: 10.1126/science.281.5376.533
  • Primary Citation of Related Structures:  
    1CKP

  • 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 synthesis and biological screening, potent inhibitors of the human CDK2-cyclin A kinase complex and of Saccharomyces cerevisiae Cdc28p were identified ...

    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
    • 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
    • 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
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CYCLIN-DEPENDENT PROTEIN KINASE 2)A298Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941
GTEx:  ENSG00000123374
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PVB
Query on PVB
Download Ideal Coordinates CCD File 
 B [auth A]PURVALANOL B
C20 H25 Cl N6 O3
ZKDXRFMOHZVXSG-HNNXBMFYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
 C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PVBIC50:  9   nM  BindingDB
PVBIC50:  6   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.55α = 90
b = 71.35β = 90
c = 72γ = 90
Software Package:
Software NamePurpose
CCP4model building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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