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PDBsum entry 1ckp

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Hormone/growth factor PDB id
1ckp
Jmol
Contents
Protein chain
279 a.a. *
Ligands
PVB
EDO
Waters ×91
* Residue conservation analysis
PDB id:
1ckp
Name: Hormone/growth factor
Title: Human cyclin dependent kinase 2 complexed with the inhibitor purvalanol b
Structure: Protein (cyclin-dependent protein kinase 2). Chain: a. Synonym: cdk2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell_line: sf9. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.
Resolution:
2.05Å     R-factor:   0.192     R-free:   0.260
Authors: N.S.Gray,A.M.W.H.Thunnissen,P.G.Schultz,S.H.Kim
Key ref:
N.S.Gray et al. (1998). Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Science, 281, 533-538. PubMed id: 9677190 DOI: 10.1126/science.281.5376.533
Date:
14-Jul-98     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2
Seq:
Struc:
298 a.a.
279 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.22  - Cyclin-dependent kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
=
ADP
Bound ligand (Het Group name = PVB)
matches with 50.00% similarity
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cyclin-dependent protein kinase holoenzyme complex   15 terms 
  Biological process     regulation of gene silencing   27 terms 
  Biochemical function     nucleotide binding     12 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.281.5376.533 Science 281:533-538 (1998)
PubMed id: 9677190  
 
 
Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors.
N.S.Gray, L.Wodicka, A.M.Thunnissen, T.C.Norman, S.Kwon, F.H.Espinoza, D.O.Morgan, G.Barnes, S.LeClerc, L.Meijer, S.H.Kim, D.J.Lockhart, P.G.Schultz.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. (A) Scheme for the combinatorial synthesis of 2,6,9-trisubstituted purines from a 2-, 6-, or 9-linked purine scaffold^ with amination and alkylation chemistries. Chemical structures of CDK inhibitors (B) flavopiridol (C) olomoucine^ and roscovitine, and (D) purvalanol A and B and (E) 52 and 52Me.
Figure 2.
Fig. 2. (A) Purvalanol B bound to CDK2 (black sticks, principal conformation only) is compared with bound (1) olomoucine^ (white sticks) and bound roscovitine (orange sticks), (2) bound flavopiridol (green sticks), and (3) bound ATP (yellow sticks). The comparisons are based on superposition of the C atoms of CDK2. The ligands are shown in ball-and-stick representation with carbon atoms colored white, nitrogen atoms colored blue, oxygen atoms colored red, phosphorous atoms colored violet, and^ the chlorine atom of purvalanol colored green. (B) Schematic^ drawing of CDK2-purvalanol B interactions. Protein side chain contacts are indicated by lines connecting the respective residue^ box and interactions to main chain atoms are shown as lines to the specific main chain atoms. Van der Waals contacts are indicated^ by thin dotted lines, and H bonds by dashed lines. For H bonds the distances between the nonhydrogen atoms are indicated in angstroms. W, water.
 
  The above figures are reprinted by permission from the AAAs: Science (1998, 281, 533-538) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB codes: 2p0c 3bpr 3brb
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Cyclin-dependent kinase inhibitors enhance the resolution of inflammation by promoting inflammatory cell apoptosis.
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The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors.
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PDB codes: 2bdf 2bdj
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Integrated microfluidic biochips for DNA microarray analysis.
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Rational design of inhibitors that bind to inactive kinase conformations.
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Small-molecule kinase-inhibitor target assessment.
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Epistasis analysis with global transcriptional phenotypes.
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Target-family-oriented focused libraries for kinases--conceptual design aspects and commercial availability.
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Latent and lytic Epstein-Barr virus replication strategies.
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New weakly expressed cell cycle-regulated genes in yeast.
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Slowed N-type calcium channel (CaV2.2) deactivation by the cyclin-dependent kinase inhibitor roscovitine.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.