+Open data
-Basic information
Entry | Database: PDB / ID: 2vv9 | ||||||
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Title | CDK2 in complex with an imidazole piperazine | ||||||
Components | CELL DIVISION PROTEIN KINASE 2 | ||||||
Keywords | TRANSFERASE / KINASE / MITOSIS / CELL CYCLE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL DIVISION / PHOSPHOPROTEIN / PHOSPHORYLATION / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation ...cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cajal body / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / potassium ion transport / G1/S transition of mitotic cell cycle / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / DNA replication / transcription regulator complex / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Acton, D.G. / Anderson, M. / Andrews, D.M. / Barker, A.J. / Brassington, C.A. / Finlay, M.R. / Fisher, E. / Gerhardt, S. / Graham, M.A. / Green, C.P. ...Acton, D.G. / Anderson, M. / Andrews, D.M. / Barker, A.J. / Brassington, C.A. / Finlay, M.R. / Fisher, E. / Gerhardt, S. / Graham, M.A. / Green, C.P. / Heaton, D.W. / Loddick, S.A. / Morgentin, R. / Read, J. / Roberts, A. / Stanway, J. / Tucker, J.A. / Weir, H.M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Imidazole Piperazines: Sar and Development of a Potent Class of Cyclin-Dependent Kinase Inhibitors with a Novel Binding Mode. Authors: Finlay, M.R. / Acton, D.G. / Andrews, D.M. / Barker, A.J. / Dennis, M. / Fisher, E. / Graham, M.A. / Green, C.P. / Heaton, D.W. / Karoutchi, G. / Loddick, S.A. / Morgentin, R. / Roberts, A. ...Authors: Finlay, M.R. / Acton, D.G. / Andrews, D.M. / Barker, A.J. / Dennis, M. / Fisher, E. / Graham, M.A. / Green, C.P. / Heaton, D.W. / Karoutchi, G. / Loddick, S.A. / Morgentin, R. / Roberts, A. / Tucker, J.A. / Weir, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vv9.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vv9.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vv9 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vv9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34002.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ACETYLATION AT N-TERMINAL METHIONINE / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-IM9 / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | ACETYL GROUP (ACE): ACETYLATIO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 8% PEG 3350, 0.1M HEPES PH 7.5, 0.05M AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM-4 / Detector: CCD / Date: Mar 11, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→27.52 Å / Num. obs: 21456 / % possible obs: 97.3 % / Observed criterion σ(I): 3.7 / Redundancy: 2.67 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.05 |
Reflection shell | Resolution: 1.9→1.92 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.8 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE CDK2 STRUCTURE Resolution: 1.9→27.52 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.115 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE-CHAINS OF DISORDERED RESIDUES HAVE BEEN TRUNCATED TO CBETA
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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: 22.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→27.52 Å
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