+Open data
-Basic information
Entry | Database: PDB / ID: 3ezr | ||||||
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Title | CDK-2 with indazole inhibitor 17 bound at its active site | ||||||
Components | Cell division protein kinase 2 | ||||||
Keywords | TRANSFERASE/Transferase inhibitor / KINASE / PKC / PROTEIN KINASE / INHIBITOR / ATP-binding / Cell cycle / Cell division / Mitosis / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Transferase-Transferase inhibitor complex | ||||||
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 / DNA Damage/Telomere Stress Induced Senescence / G1/S transition of mitotic cell cycle / 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 / DNA replication / Ras protein signal transduction / 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 / Resolution: 1.9 Å | ||||||
Authors | Kiefer, J.R. / Day, J.E. / Caspers, N.L. / Mathis, K.J. / Kretzmer, K.K. / Weinberg, R.A. / Reitz, B.A. / Stegeman, R.A. / Trujillo, J.I. / Huang, W. ...Kiefer, J.R. / Day, J.E. / Caspers, N.L. / Mathis, K.J. / Kretzmer, K.K. / Weinberg, R.A. / Reitz, B.A. / Stegeman, R.A. / Trujillo, J.I. / Huang, W. / Thorarensen, A. / Xing, L. / Wrightstone, A. / Christine, L. / Compton, R. / Li, X. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: 2-(6-Phenyl-1H-indazol-3-yl)-1H-benzo[d]imidazoles: Design and synthesis of a potent and isoform selective PKC-zeta inhibitor Authors: Trujillo, J.I. / Kiefer, J.R. / Huang, W. / Thorarensen, A. / Xing, L. / Caspers, N.L. / Day, J.E. / Mathis, K.J. / Kretzmer, K.K. / Reitz, B.A. / Weinberg, R.A. / Stegeman, R.A. / ...Authors: Trujillo, J.I. / Kiefer, J.R. / Huang, W. / Thorarensen, A. / Xing, L. / Caspers, N.L. / Day, J.E. / Mathis, K.J. / Kretzmer, K.K. / Reitz, B.A. / Weinberg, R.A. / Stegeman, R.A. / Wrightstone, A. / Christine, L. / Compton, R. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ezr.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ezr.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 3ezr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/3ezr ftp://data.pdbj.org/pub/pdb/validation_reports/ez/3ezr | HTTPS FTP |
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-Related 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: 34120.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 14% PEG 4K, 50mM Hepes pH 7.5, 50mM ammonium acetate, 10 mM DTT, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 28, 2007 / Details: Osmic Blue Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18.79 Å / Num. all: 22762 / Num. obs: 22591 / Limit h max: 28 / Limit h min: 0 / Limit k max: 37 / Limit k min: 0 / Limit l max: 38 / Limit l min: 0 |
Reflection scale | Group code: 1 |
-Processing
Software |
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Refinement | Resolution: 1.9→18.79 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 3.776 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.2 Å2 / Biso mean: 44.822 Å2 / Biso min: 28.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→18.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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