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- PDB-9ks9: Crystal structure of MerTK kinase domain in complex with compound 6 -
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Open data
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Basic information
Entry | Database: PDB / ID: 9ks9 | ||||||
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Title | Crystal structure of MerTK kinase domain in complex with compound 6 | ||||||
![]() | Tyrosine-protein kinase Mer | ||||||
![]() | TRANSFERASE / kinase / dynamic dimer / Complex / TAM / Immune regulation / allosteric binding inhibitor / Type 2 inhibitor | ||||||
Function / homology | ![]() negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / phagocytosis / transmembrane receptor protein tyrosine kinase activity ...negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / Cell surface interactions at the vascular wall / establishment of localization in cell / receptor protein-tyrosine kinase / platelet activation / cell migration / nervous system development / cell-cell signaling / retina development in camera-type eye / spermatogenesis / cell surface receptor signaling pathway / protein phosphorylation / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular space / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peng, Y.H. / Lee, L.C. / Hsueh, C.C. / Wu, S.Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure-Based Design of Potent and Selective MerTK Inhibitors by Modulating the Conformation of alpha C Helix. Authors: Peng, Y.H. / Li, M.C. / Yen, W.C. / Yeh, T.K. / Hsueh, C.C. / Kuo, F.M. / Lai, Y.L. / Chang, L. / Lee, L.C. / Chen, P.Y. / Yen, K.J. / Chang, T.Y. / Sun, H.Y. / Chang, C.Y. / Hsieh, S.H. / ...Authors: Peng, Y.H. / Li, M.C. / Yen, W.C. / Yeh, T.K. / Hsueh, C.C. / Kuo, F.M. / Lai, Y.L. / Chang, L. / Lee, L.C. / Chen, P.Y. / Yen, K.J. / Chang, T.Y. / Sun, H.Y. / Chang, C.Y. / Hsieh, S.H. / Yang, C.M. / Hsieh, H.P. / Wu, S.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 | ![]() | 119.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 914.4 KB | Display | ![]() |
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Full document | ![]() | 920.8 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9kryC ![]() 9krzC ![]() 3tcpS S: Starting model for refinement C: citing same article ( |
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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: 33856.230 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Variant (production host): BL21(DE3)pLysS Escherichia coli pLysS References: UniProt: Q12866, receptor protein-tyrosine kinase #2: Chemical | Mass: 613.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H24FN7O4 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 24% PEG 200, 0.05 M Calcium chloride dehydrate, 0.1 M MES monohydrate pH 6.4 PH range: 6.1-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 25, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45.675 Å / Num. obs: 14613 / % possible obs: 92.8163 % / Redundancy: 9.8 % / CC1/2: 0.992 / Rrim(I) all: 0.125 / Net I/av σ(I): 14.39 / Net I/σ(I): 14.39 |
Reflection shell | Resolution: 2.8→3.53 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 6.77 / Num. unique obs: 2383 / CC1/2: 0.976 / Rrim(I) all: 0.253 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TCP Resolution: 2.8→34.28 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 28.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→34.28 Å
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Refine LS restraints |
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LS refinement shell |
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