2A4L

Human cyclin-dependent kinase 2 in complex with roscovitine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 518-526


  • PubMed Abstract: 
  • Cyclin-dependent kinases (cdk) control the cell division cycle (cdc). These kinases and their regulators are frequently deregulated in human tumours. A potent inhibitor of cdks, roscovitine [2-(1-ethyl-2-hydroxyethylamino)-6-benzylamino-9-isopropylpu ...

    Cyclin-dependent kinases (cdk) control the cell division cycle (cdc). These kinases and their regulators are frequently deregulated in human tumours. A potent inhibitor of cdks, roscovitine [2-(1-ethyl-2-hydroxyethylamino)-6-benzylamino-9-isopropylpurin e], was identified by screening a series of C2,N6,N9-substituted adenines on purified cdc2/cyclin B. Roscovitine displays high efficiency and high selectivity (Meijer, L., Borgne, A., Mulner, O., Chong, J. P. J., Blow, J. J., Inagaki, N., Inagaki, M., Delcros, J.-G. & Moulinoux, J.-P. (1997) Eur. J. Biochem. 243, 527-536). It behaves as a competitive inhibitor for ATP binding to cdc2. We determined the crystal structure of a complex between cdk2 and roscovitine at 0.24-nm (2.4 A) resolution and refined to an Rfactor of 0.18. The purine portion of the inhibitor binds to the adenine binding pocket of cdk2. The position of the benzyl ring group of the inhibitor enables the inhibitor to make contacts with the enzyme not observed in the ATP-complex structure. Analysis of the position of this benzyl ring explains the specificity of roscovitine in inhibiting cdk2. The structure also reveals that the (R)-stereoisomer of roscovitine is bound to cdk2. The (R)-isomer is about twice as potent in inhibiting cdc2/cyclin B than the (S)-isomer. Results from structure/activity studies and from analysis of the cdk2/roscovitine complex crystal structure should allow the design of even more potent cdk inhibitors.


    Related Citations: 
    • 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
    • Structural basis for specificity and potency of a flavonoid inhibitor of human CDK2, a cell cycle kinase
      De Azevedo Jr., W.F.,Mueller-Dieckman, H.J.,Schulze-Gahmen, U.,Worland, P.J.,Sausville, E.,Kim, S.H.
      (1996) Proc.Natl.Acad.Sci.USA 93: 2735


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homo sapiens cyclin-dependent 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RRC
Query on RRC

Download SDF File 
Download CCD File 
A
R-ROSCOVITINE
C19 H26 N6 O
BTIHMVBBUGXLCJ-OAHLLOKOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.307α = 90.00
b = 73.069β = 90.00
c = 54.284γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description