2A4L

Human cyclin-dependent kinase 2 in complex with roscovitine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


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

  • DOI: 10.1111/j.1432-1033.1997.0518a.x
  • Primary Citation of Related Structures:  
    2A4L

  • 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-isopropylpurin e], was identified by screening a series of C2,N6,N9-substituted adenines on purified cdc2/cyclin B ...

    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: 
    • 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 U S A 93: 2735
    • 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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homo sapiens cyclin-dependent kinase 2A298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RRC (Subject of Investigation/LOI)
Query on RRC

Download Ideal Coordinates CCD File 
B [auth A]R-ROSCOVITINE
C19 H26 N6 O
BTIHMVBBUGXLCJ-OAHLLOKOSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
RRC BindingDB:  2A4L Ki: 250 (nM) from 1 assay(s)
Kd: min: 2900, max: 3400 (nM) from 2 assay(s)
IC50: min: 0.1, max: 708 (nM) from 18 assay(s)
PDBBind:  2A4L IC50: 400 (nM) from 1 assay(s)
Binding MOAD:  2A4L IC50: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.307α = 90
b = 73.069β = 90
c = 54.284γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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