+Open data
-Basic information
Entry | Database: PDB / ID: 4as0 | ||||||
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Title | Cyclometalated Phthalimides as Protein Kinase Inhibitors | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE PIM-1 | ||||||
Keywords | TRANSFERASE / PIM1 / OCTASPORINE / RUTHENIUM / KINASE INHIBITOR | ||||||
Function / homology | Function and homology information positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / positive regulation of cyclin-dependent protein serine/threonine kinase activity / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / Signaling by FLT3 fusion proteins ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / positive regulation of cyclin-dependent protein serine/threonine kinase activity / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / nucleolus / apoptotic process / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Blanck, S. / Geisselbrecht, Y. / Middel, S. / Mietke, T. / Harms, K. / Essen, L.-O. / Meggers, E. | ||||||
Citation | Journal: Dalton Trans / Year: 2012 Title: Bioactive Cyclometalated Phthalimides: Design, Synthesis and Kinase Inhibition. Authors: Blanck, S. / Geisselbrecht, Y. / Kraling, K. / Middel, S. / Mietke, T. / Harms, K. / Essen, L.-O. / Meggers, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4as0.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4as0.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 4as0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4as0_validation.pdf.gz | 922.6 KB | Display | wwPDB validaton report |
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Full document | 4as0_full_validation.pdf.gz | 925.4 KB | Display | |
Data in XML | 4as0_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4as0_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/4as0 ftp://data.pdbj.org/pub/pdb/validation_reports/as/4as0 | HTTPS FTP |
-Related structure data
Related structure data | 3bwfS S: Starting model for refinement |
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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: 31417.654 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: P11309, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-RPS / |
#3: Water | ChemComp-HOH / |
Sequence details | ISOFORM-2 MUTATION R250G (GI 33304198) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.49 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 200 MM SODIUM CITRATE, 100 MM HEPES, 30 % MPD, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2011 Details: PT COATED MIRRORS IN A KIRKPATRICK-BAEZ (KB) GEOMETRY |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 20098 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.62 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.81 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BWF Resolution: 2.3→24.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.164 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.991 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→24.8 Å
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