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- PDB-8afr: Pim1 in complex with 4-((6-hydroxybenzofuran-3-yl)methyl)benzoic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8afr | ||||||
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Title | Pim1 in complex with 4-((6-hydroxybenzofuran-3-yl)methyl)benzoic acid and Pimtide | ||||||
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![]() | TRANSFERASE / SERINE KINASE / KINASE / COMPLEX / PIM1 / PIM / PIM-1 / INHIBITOR / TUMORIGENISIS / CANCER / PIMTIDE / PROTO ONCOGEN / ATP / PHOSPHORYLATION / APOPTOSIS / CELL CYCLE | ||||||
Function / homology | ![]() 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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / 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 | ![]() Synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hochban, P.M.M. / Heine, A. / Diederich, W.E. | ||||||
Funding support | 1items
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![]() | ![]() Title: Pose, duplicate, then elaborate: Steps towards increased affinity for inhibitors targeting the specificity surface of the Pim-1 kinase. Authors: Heyder, L. / Hochban, P.M.M. / Taylor, C. / Chevillard, F. / Siefker, C. / Iking, C. / Borchardt, H. / Aigner, A. / Klebe, G. / Heine, A. / Kolb, P. / Diederich, W.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153 KB | Display | ![]() |
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PDB format | ![]() | 99 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 684.6 KB | Display | ![]() |
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Full document | ![]() | 684.5 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qb2C ![]() 7qfmC ![]() 7z6uC ![]() 5ndtS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35356.141 Da / Num. of mol.: 1 / Mutation: R250G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11309, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
#3: Chemical | ChemComp-M0F / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM bis-tris-propane (pH7.0), 10 % ethylene glycol, 0.3% DMSO, 20% PEG3350, 200 mM LiCl PH range: 6.8 - 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019 / Details: Sagitally bended Si111-crystal |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→48.22 Å / Num. obs: 22836 / % possible obs: 98.1 % / Redundancy: 13.9 % / Biso Wilson estimate: 40.22 Å2 / CC1/2: 1 / Rsym value: 0.055 / Net I/σ(I): 32.97 |
Reflection shell | Resolution: 2.15→2.28 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 5.12 / Num. unique obs: 3583 / CC1/2: 0.963 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NDT Resolution: 2.15→48.22 Å / SU ML: 0.1586 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.9775 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→48.22 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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