Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34471.46 
• Atom Count: 2290 
• Residue Count: 298 
• Unique protein chains: 1

1CKP

HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR PURVALANOL B

• DOI: 10.2210/pdb1CKP/pdb

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 1998-07-14 Released: 1999-01-13 
• Deposition Author(s): Gray, N.S., Thunnissen, A.M.W.H., Schultz, P.G., Kim, S.H.

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Experimental Data Snapshot

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

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: 9677190 


• 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. 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.

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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
• 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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (CYCLIN-DEPENDENT PROTEIN KINASE 2)	A	298	Homo sapiens	Mutation(s): 0  Gene 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
PVB	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PVB	IC50: 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 = 53.550	α = 90.00
b = 71.350	β = 90.00
c = 72.000	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	refinement
CCP4	model building
DENZO	data reduction
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-14 
• Released Date: 1999-01-13 
• Deposition Author(s): Gray, N.S., Thunnissen, A.M.W.H., Schultz, P.G., Kim, S.H.

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