|Entry||Database: PDB / ID: 1y91|
|Title||Crystal structure of human CDK2 complexed with a pyrazolo[1,5-a]pyrimidine inhibitor|
|Components||Cell division protein kinase 2|
|Keywords||TRANSFERASE / Serine/Threonine protein kinase / CDK2 / ATP-binding / Cell cycle / mitosis / phosphorylation / pyrazolopyrimidine inhibitor|
|Function / homology|
Function and homology information
Orc1 removal from chromatin / G0 and Early G1 / Activation of ATR in response to replication stress / Regulation of APC/C activators between G1/S and early anaphase / SCF(Skp2)-mediated degradation of p27/p21 / Senescence-Associated Secretory Phenotype (SASP) / DNA Damage/Telomere Stress Induced Senescence / Processing of DNA double-strand break ends / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of TP53 Degradation ...Orc1 removal from chromatin / G0 and Early G1 / Activation of ATR in response to replication stress / Regulation of APC/C activators between G1/S and early anaphase / SCF(Skp2)-mediated degradation of p27/p21 / Senescence-Associated Secretory Phenotype (SASP) / DNA Damage/Telomere Stress Induced Senescence / Processing of DNA double-strand break ends / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of TP53 Degradation / G2 Phase / Regulation of TP53 Activity through Phosphorylation / Activation of the pre-replicative complex / Factors involved in megakaryocyte development and platelet production / Meiotic recombination / PTK6 Regulates Cell Cycle / CDK-mediated phosphorylation and removal of Cdc6 / Cyclin A:Cdk2-associated events at S phase entry / p53-Dependent G1 DNA Damage Response / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin E associated events during G1/S transition / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / Cajal body / cellular response to nitric oxide / mitotic G1 DNA damage checkpoint / cyclin binding / regulation of gene silencing / potassium ion transport / meiotic cell cycle / chromosome, telomeric region / G1/S transition of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Ras protein signal transduction / transcription factor complex / G2/M transition of mitotic cell cycle / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / centrosome / cell division / DNA repair / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / positive regulation of cell population proliferation / positive regulation of transcription, DNA-templated / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile. / Protein kinase-like domain superfamily / Protein kinase domain / Protein kinase, ATP binding site / Protein kinase domain / Protein kinases ATP-binding region signature.
Cyclin-dependent kinase 2
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å|
|Authors||Williamson, D.S. / Parratt, M.J. / Torrance, C.J. / Bower, J.F. / Moore, J.D. / Richardson, C.M. / Dokurno, P. / Cansfield, A.D. / Francis, G.L. / Hebdon, R.J. / Howes, R. / Jackson, P.S. / Lockie, A.M. / Murray, J.B. / Nunns, C.L. / Powles, J. / Robertson, A. / Surgenor, A.E.|
|Citation||Journal: Bioorg.Med.Chem.Lett. / Year: 2005|
Title: Structure-guided design of pyrazolo[1,5-a]pyrimidines as inhibitors of human cyclin-dependent kinase 2.
Authors: Williamson, D.S. / Parratt, M.J. / Bower, J.F. / Moore, J.D. / Richardson, C.M. / Dokurno, P. / Cansfield, A.D. / Francis, G.L. / Hebdon, R.J. / Howes, R. / Jackson, P.S. / Lockie, A.M. / Murray, J.B. / Nunns, C.L. / Powles, J. / Robertson, A. / Surgenor, A.E. / Torrance, C.J.
SummaryFull reportAbout validation report
|Date||Deposition: Dec 14, 2004 / Release: Feb 8, 2005|
|Structure viewer||Molecule: |
Downloads & links
A: Cell division protein kinase 2
|#1: Protein/peptide|| |
Mass: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P24941, EC: 184.108.40.206
|#2: Chemical|| ChemComp-CT9 / |
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2 Å3/Da / Density % sol: 37.8 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 |
Details: Peg 3350, Hepes, Ammonium acetate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å|
|Detector||Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 9, 2003 / Details: mirrors|
|Radiation||Monochromator: MSC/Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.5418 Å / Relative weight: 1|
|Reflection||Resolution: 1.8→30 Å / Num. all: 24371 / Num. obs: 24371 / % possible obs: 92.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.65 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.8|
|Reflection shell||Resolution: 1.8→1.86 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2575 / % possible all: 64.2|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: pdb entry 1B39
Resolution: 2.15→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.389 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.325 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK|
|Displacement parameters||Biso mean: 39.164 Å2|
|Refinement step||Cycle: LAST / Resolution: 2.15→25 Å|
|Refine LS restraints|
Refinement-ID: X-RAY DIFFRACTION
|LS refinement shell||Resolution: 2.15→2.205 Å / Total num. of bins used: 20 |
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