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Yorodumi- PDB-4u8z: Crystal structure of MST3 with a pyrrolopyrimidine inhibitor (PF-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u8z | ||||||
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Title | Crystal structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06447475) | ||||||
Components | Serine/threonine-protein kinase 24 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / MST3 / pyrrolopyrimidine / inhibitor / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Apoptotic execution phase / FAR/SIN/STRIPAK complex / regulation of axon regeneration / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress ...Apoptotic execution phase / FAR/SIN/STRIPAK complex / regulation of axon regeneration / intrinsic apoptotic signaling pathway in response to oxidative stress / execution phase of apoptosis / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / protein phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Jasti, J. / Song, X. / Griffor, M. / Kurumbail, R.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Discovery and preclinical profiling of 3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile (PF-06447475), a highly potent, selective, brain penetrant, and in vivo active LRRK2 kinase inhibitor. Authors: Henderson, J.L. / Kormos, B.L. / Hayward, M.M. / Coffman, K.J. / Jasti, J. / Kurumbail, R.G. / Wager, T.T. / Verhoest, P.R. / Noell, G.S. / Chen, Y. / Needle, E. / Berger, Z. / Steyn, S.J. / ...Authors: Henderson, J.L. / Kormos, B.L. / Hayward, M.M. / Coffman, K.J. / Jasti, J. / Kurumbail, R.G. / Wager, T.T. / Verhoest, P.R. / Noell, G.S. / Chen, Y. / Needle, E. / Berger, Z. / Steyn, S.J. / Houle, C. / Hirst, W.D. / Galatsis, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u8z.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u8z.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 4u8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u8z_validation.pdf.gz | 770.1 KB | Display | wwPDB validaton report |
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Full document | 4u8z_full_validation.pdf.gz | 773.3 KB | Display | |
Data in XML | 4u8z_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 4u8z_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/4u8z ftp://data.pdbj.org/pub/pdb/validation_reports/u8/4u8z | HTTPS FTP |
-Related structure data
Related structure data | 4w8dC 4w8eC 3a7jS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32954.770 Da / Num. of mol.: 1 / Fragment: UNP residues 9-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STK24, MST3, STK3 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-3FE / |
#4: 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: 2.74 Å3/Da / Density % sol: 55.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl (pH 8.5), 180mM MgCl2, 5mM Manganese (II) acetate, 10-17% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→37.4 Å / Num. obs: 42612 / % possible obs: 96.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 29.42 Å2 / Rsym value: 0.03 / Net I/σ(I): 16.4 |
-Processing
Software | Name: BUSTER / Version: 2.11.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3a7j Resolution: 1.63→37.4 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9295 / SU R Cruickshank DPI: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.091 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.091
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Displacement parameters | Biso mean: 38.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.223 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.63→37.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.67 Å / Total num. of bins used: 20
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