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Yorodumi- PDB-8bjt: Structure of human PLK1 in complex with 2-Allyl-1-[6-(1-hydroxy-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bjt | ||||||
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Title | Structure of human PLK1 in complex with 2-Allyl-1-[6-(1-hydroxy-1-methyl-ethyl)-pyridin-2-yl]-6-[4-(4-methyl-piperazin-1-yl)-phenylamino]-1,2-dihydro-pyrazolo[3,4-d]pyrimidin-3-one | ||||||
Components | Serine/threonine-protein kinase PLK1 | ||||||
Keywords | TRANSFERASE / PLK1 / SELECTIVITY RESIDUES / KINASE / POLO-LIKE KINASE / STRUCTURE BASED DRUG DESIGN / ATP-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE | ||||||
Function / homology | Function and homology information Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / regulation of protein binding / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / mitotic chromosome condensation / Golgi Cisternae Pericentriolar Stack Reorganization / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / centriolar satellite / mitotic cytokinesis / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein localization to chromatin / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / peptidyl-serine phosphorylation / regulation of cell cycle / protein kinase activity / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.188 Å | ||||||
Authors | Musil, D. / Liu-Bujalski, L. | ||||||
Funding support | 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2023 Title: Selective Wee1 Inhibitors Led to Antitumor Activity In Vitro and Correlated with Myelosuppression. Authors: Guler, S. / DiPoto, M.C. / Crespo, A. / Caldwell, R. / Doerfel, B. / Grossmann, N. / Ho, K. / Huck, B. / Jones, C.C. / Lan, R. / Musil, D. / Potnick, J. / Schilke, H. / Sherer, B. / Simon, S. ...Authors: Guler, S. / DiPoto, M.C. / Crespo, A. / Caldwell, R. / Doerfel, B. / Grossmann, N. / Ho, K. / Huck, B. / Jones, C.C. / Lan, R. / Musil, D. / Potnick, J. / Schilke, H. / Sherer, B. / Simon, S. / Sirrenberg, C. / Zhang, Z. / Liu-Bujalski, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bjt.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bjt.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bjt_validation.pdf.gz | 737.2 KB | Display | wwPDB validaton report |
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Full document | 8bjt_full_validation.pdf.gz | 740.3 KB | Display | |
Data in XML | 8bjt_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 8bjt_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/8bjt ftp://data.pdbj.org/pub/pdb/validation_reports/bj/8bjt | HTTPS FTP |
-Related structure data
Related structure data | 8bjuC 2rkuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33823.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53350, polo kinase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-8X7 / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% w/v PEG4000, 0.1 M Na citrate pH 6.50, 0.6 M Mg acetate, 0.0003 M Zn acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99991 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99991 Å / Relative weight: 1 |
Reflection | Resolution: 2.188→54.29 Å / Num. obs: 7568 / % possible obs: 83.3 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.188→2.507 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 377 / CC1/2: 0.816 / Rpim(I) all: 0.312 / Rrim(I) all: 0.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2rku Resolution: 2.188→54.29 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.44
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Displacement parameters | Biso mean: 50.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.188→54.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.52 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -26.9116 Å / Origin y: 22.7693 Å / Origin z: -9.6265 Å
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Refinement TLS group | Selection details: { A|* } |