2A0C | pdb_00002a0c

Human CDK2 in complex with olomoucine II, a novel 2,6,9-trisubstituted purine cyclin-dependent kinase inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.244 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.191 (Depositor) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Antiproliferative activity of olomoucine II, a novel 2,6,9-trisubstituted purine cyclin-dependent kinase inhibitor

Krystof, V.McNae, I.W.Walkinshaw, M.D.Fischer, P.M.Muller, P.Vojtesek, B.Orsag, M.Havlicek, L.Strnad, M.

(2005) Cell Mol Life Sci 62: 1763-1771

  • DOI: https://doi.org/10.1007/s00018-005-5185-1
  • Primary Citation Related Structures: 
    2A0C

  • PubMed Abstract: 

    The study describes the protein kinase selectivity profile, as well as the binding mode of olomoucine II in the catalytic cleft of CDK2, as determined from cocrystal analysis. Apart from the main cell cycle-regulating kinase CDK2, olomoucine II exerts specificity for CDK7 and CDK9, with important functions in the regulation of RNA transcription. In vitro anticancer activity of the inhibitor in a panel of tumor cell lines shows a wide potency range with a slight preference for cells harboring a wild-type p53 gene. Cell-based assays confirmed activation of p53 protein levels and events leading to accumulation of p21(WAF1). Additionally, in olomoucine II-treated cells, Mdm2 was found to form a complex with the ribosomal protein L11, which inhibits Mdm2 ubiquitin ligase function. We conclude that perturbations in RNA synthesis may lead to activation of p53 and that this contributes to the antiproliferative potency of cyclindependent kinase inhibitors.


  • Organizational Affiliation
    • Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany AS CR, Slechtitelů 11, 783 71, Olomouc, The Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 34.35 kDa 
  • Atom Count: 2,531 
  • Modeled Residue Count: 294 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division protein kinase 2A [auth X]298Homo sapiensMutation(s): 0 
Gene Names: CDK2
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
GTEx:  ENSG00000123374 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CK9

Query on CK9



Download:Ideal Coordinates CCD File
B [auth X]2-{[(2-{[(1R)-1-(HYDROXYMETHYL)PROPYL]AMINO}-9-ISOPROPYL-9H-PURIN-6-YL)AMINO]METHYL}PHENOL
C19 H26 N6 O2
NDUVSANREQEDRE-CQSZACIVSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.244 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.191 (Depositor) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.242α = 90
b = 70.945β = 90
c = 71.869γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    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: 2024-03-13
    Changes: Data collection, Database references, Derived calculations