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Yorodumi- PDB-4wrs: Crystal structure of human Pim-1 kinase in complex with an azaspi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wrs | ||||||
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Title | Crystal structure of human Pim-1 kinase in complex with an azaspiro pyrazinyl-indazole inhibitor. | ||||||
Components | Serine/threonine-protein kinase pim-1 | ||||||
Keywords | transferase/transferase inhibitor / TRANSFERASE / serine/threonine protein kinase / transferase-transferase inhibitor complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Mohr, C. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2015 Title: The discovery of novel 3-(pyrazin-2-yl)-1H-indazoles as potent pan-Pim kinase inhibitors. Authors: Wang, H.L. / Cee, V.J. / Chavez, F. / Lanman, B.A. / Reed, A.B. / Wu, B. / Guerrero, N. / Lipford, J.R. / Sastri, C. / Winston, J. / Andrews, K.L. / Huang, X. / Lee, M.R. / Mohr, C. / Xu, Y. ...Authors: Wang, H.L. / Cee, V.J. / Chavez, F. / Lanman, B.A. / Reed, A.B. / Wu, B. / Guerrero, N. / Lipford, J.R. / Sastri, C. / Winston, J. / Andrews, K.L. / Huang, X. / Lee, M.R. / Mohr, C. / Xu, Y. / Zhou, Y. / Tasker, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wrs.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wrs.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wrs_validation.pdf.gz | 896.4 KB | Display | wwPDB validaton report |
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Full document | 4wrs_full_validation.pdf.gz | 898.3 KB | Display | |
Data in XML | 4wrs_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4wrs_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/4wrs ftp://data.pdbj.org/pub/pdb/validation_reports/wr/4wrs | HTTPS FTP |
-Related 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: 33064.422 Da / Num. of mol.: 1 / Fragment: unp residues 124-396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli) References: UniProt: P11309, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-3U1 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.0M LiCl, 0.1M TRIS, 20% PEG6K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 24, 2014 |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 22333 / % possible obs: 98.4 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 4.95 / % possible all: 97 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.215 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.159 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 44.684 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→29.75 Å
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