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- PDB-6l14: 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: 6l14 | ||||||
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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 / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 52.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kziC ![]() 6l11C ![]() 6l12C ![]() 6l13C ![]() 6l15C ![]() 6l16C ![]() 6l17C ![]() 1ywvS S: Starting model for refinement 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, ![]() |
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#2: Chemical | ChemComp-E2L / |
#3: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.87 % |
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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: Y |
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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![]() |
Reflection | Resolution: 1.95→85.24 Å / Num. obs: 32642 / % possible obs: 99.8 % / Redundancy: 11.2 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 44.72 |
Reflection shell | Resolution: 1.95→1.998 Å / Rmerge(I) obs: 1.038 / Num. unique obs: 2272 / CC1/2: 0.787 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1YWV Resolution: 1.95→85.24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.112 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.89 Å2 / Biso mean: 42.887 Å2 / Biso min: 25.35 Å2
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Refinement step | Cycle: final / Resolution: 1.95→85.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→1.998 Å / Rfactor Rfree error: 0
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