[English] 日本語
Yorodumi- PDB-4i5p: Selective & Brain-Permeable Polo-like Kinase-2 (Plk-2) Inhibitors... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i5p | ||||||
---|---|---|---|---|---|---|---|
Title | Selective & Brain-Permeable Polo-like Kinase-2 (Plk-2) Inhibitors that Reduce -Synuclein Phosphorylation in Rat Brain | ||||||
Components | Serine/threonine-protein kinase PLK2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Polo-like kinase-2 (Plk-2) / Synuclein / Parkinson's disease / Kinase Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of centriole replication / Rap protein signal transduction / negative regulation of apoptotic process in bone marrow cell / polo kinase / ATP-dependent protein binding / long-term synaptic depression / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / CD163 mediating an anti-inflammatory response / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cellular senescence ...regulation of centriole replication / Rap protein signal transduction / negative regulation of apoptotic process in bone marrow cell / polo kinase / ATP-dependent protein binding / long-term synaptic depression / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / CD163 mediating an anti-inflammatory response / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cellular senescence / positive regulation of autophagy / negative regulation of inflammatory response to antigenic stimulus / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / centriole / negative regulation of angiogenesis / mitotic spindle organization / long-term synaptic potentiation / regulation of synaptic plasticity / G1/S transition of mitotic cell cycle / kinetochore / memory / spindle pole / positive regulation of protein catabolic process / peptidyl-serine phosphorylation / positive regulation of canonical NF-kappaB signal transduction / Ras protein signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / chromatin / negative regulation of apoptotic process / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.738 Å | ||||||
Authors | Aubele, D.L. / Hom, R.K. / Adler, M. / Galemmo Jr., R.A. / Bowers, S. / Truong, A.P. / Pan, H. / Beroza, P. | ||||||
Citation | Journal: Chemmedchem / Year: 2013 Title: Selective and brain-permeable polo-like kinase-2 (Plk-2) inhibitors that reduce alpha-synuclein phosphorylation in rat brain. Authors: Aubele, D.L. / Hom, R.K. / Adler, M. / Galemmo, R.A. / Bowers, S. / Truong, A.P. / Pan, H. / Beroza, P. / Neitz, R.J. / Yao, N. / Lin, M. / Tonn, G. / Zhang, H. / Bova, M.P. / Ren, Z. / Tam, ...Authors: Aubele, D.L. / Hom, R.K. / Adler, M. / Galemmo, R.A. / Bowers, S. / Truong, A.P. / Pan, H. / Beroza, P. / Neitz, R.J. / Yao, N. / Lin, M. / Tonn, G. / Zhang, H. / Bova, M.P. / Ren, Z. / Tam, D. / Ruslim, L. / Baker, J. / Diep, L. / Fitzgerald, K. / Hoffman, J. / Motter, R. / Fauss, D. / Tanaka, P. / Dappen, M. / Jagodzinski, J. / Chan, W. / Konradi, A.W. / Latimer, L. / Zhu, Y.L. / Sham, H.L. / Anderson, J.P. / Bergeron, M. / Artis, D.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4i5p.cif.gz | 83 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4i5p.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 4i5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/4i5p ftp://data.pdbj.org/pub/pdb/validation_reports/i5/4i5p | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 35832.188 Da / Num. of mol.: 1 / Fragment: PLK2 kinase domain / Mutation: C83S, V87T, A119S, A216S, C259A, C291S, L335T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLK2, SNK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYY3, polo kinase |
---|---|
#2: Chemical | ChemComp-1D1 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % |
---|---|
Crystal grow | Temperature: 277 K / Method: evaporation / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, 0.8 M sodium formate, 19% PEG 3350, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9788 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.738→39.16 Å / Num. all: 30740 / Num. obs: 23547 / % possible obs: 76.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.738→1.783 Å / % possible all: 7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.738→39.16 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.894 / SU B: 3.242 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.188 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.625 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.738→39.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.738→1.783 Å / Total num. of bins used: 20
|