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- PDB-6l13: Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6l13 | ||||||
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Title | Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC derivatives | ||||||
![]() | Serine/threonine-protein kinase pim-1 | ||||||
![]() | TRANSFERASE/INHIBITOR / Pim-1 kinase / 10-DEBC / TRANSFERASE-INHIBITOR complex | ||||||
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 / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, W. / Xie, Y. / Cao, R. / Huang, N. / Zhou, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors. Authors: Li, G. / Zhang, W. / Xie, Y. / Li, Y. / Cao, R. / Zheng, G. / Huang, N. / Zhou, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.8 KB | Display | ![]() |
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PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 762.3 KB | Display | ![]() |
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Full document | ![]() | 763.8 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kziC ![]() 6l11C ![]() 6l12C ![]() 6l14C ![]() 6l15C ![]() 6l16C ![]() 6l17C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33292.719 Da / Num. of mol.: 1 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: Chemical | ChemComp-E2F / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.4M potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→84.83 Å / Num. obs: 21123 / % possible obs: 99.6 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.241→2.299 Å / Rmerge(I) obs: 0.666 / Num. unique obs: 2123 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 106.75 Å2 / Biso mean: 35.482 Å2 / Biso min: 19.25 Å2
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Refinement step | Cycle: final / Resolution: 2.24→84.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.241→2.299 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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