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Yorodumi- PDB-6ykd: Human Pim-1 kinase in complex with an inhibitor identified by vir... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ykd | ||||||
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Title | Human Pim-1 kinase in complex with an inhibitor identified by virtual screening | ||||||
Components | Serine/threonine-protein kinase pim-1 | ||||||
Keywords | APOPTOSIS / KINASE / CANCER / TRANSFERASE / ATP-BINDING / virtual screening | ||||||
Function / homology | Function and homology information positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / 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 / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å | ||||||
Authors | Schneider, P. / Welin, M. / Svensson, B. / Walse, B. / Schneider, G. | ||||||
Citation | Journal: Mol Inform / Year: 2020 Title: Virtual Screening and Design with Machine Intelligence Applied to Pim-1 Kinase Inhibitors. Authors: Schneider, P. / Welin, M. / Svensson, B. / Walse, B. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ykd.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ykd.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ykd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ykd_validation.pdf.gz | 855.3 KB | Display | wwPDB validaton report |
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Full document | 6ykd_full_validation.pdf.gz | 858.9 KB | Display | |
Data in XML | 6ykd_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 6ykd_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/6ykd ftp://data.pdbj.org/pub/pdb/validation_reports/yk/6ykd | HTTPS FTP |
-Related structure data
Related structure data | 3r04S 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: 37632.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The biological sequence starts at M17. His (-11) - His (-8) is part of the Histidine tag. Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P11309, non-specific serine/threonine protein kinase | ||||||
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#2: Chemical | ChemComp-OWB / ~{ | ||||||
#3: Chemical | #4: Chemical | ChemComp-ACT / | #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: 3.02 Å3/Da / Density % sol: 59.25 % |
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Crystal grow | Temperature: 277 K / Method: counter-diffusion / pH: 6.3 / Details: 0.1 M imidazole pH 6.3 1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→19.61 Å / Num. obs: 36740 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.862→1.894 Å / Redundancy: 6 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1859 / CC1/2: 0.853 / Rpim(I) all: 0.248 / Rrim(I) all: 0.638 / % possible all: 99.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R04 Resolution: 1.86→19.61 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.377 / SU ML: 0.069 / SU R Cruickshank DPI: 0.0965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.1 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.68 Å2 / Biso mean: 43.51 Å2 / Biso min: 26.42 Å2
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Refinement step | Cycle: final / Resolution: 1.86→19.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.861→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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