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- PDB-7ab1: Crystal structure of MerTK kinase domain in complex with Gilteritinib -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ab1 | ||||||
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Title | Crystal structure of MerTK kinase domain in complex with Gilteritinib | ||||||
![]() | Tyrosine-protein kinase Mer | ||||||
![]() | TRANSFERASE / tyrosine kinase inhibitor / structure-based drug design / type 1 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 / positive regulation of phagocytosis ...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 / positive regulation of phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / establishment of localization in cell / Cell surface interactions at the vascular wall / receptor protein-tyrosine kinase / platelet activation / cell migration / cell-cell signaling / retina development in camera-type eye / nervous system development / spermatogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / receptor complex / protein phosphorylation / extracellular space / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pflug, A. / Schimpl, M. / McCoull, W. / Nissink, J.W.M. / Overman, R.C. / Rawlins, P.B. / Truman, C. / Underwood, E. / Warwicker, J. / Winter-Holt, J. | ||||||
![]() | ![]() Title: A-loop interactions in Mer tyrosine kinase give rise to inhibitors with two-step mechanism and long residence time of binding. Authors: Pflug, A. / Schimpl, M. / Nissink, J.W.M. / Overman, R.C. / Rawlins, P.B. / Truman, C. / Underwood, E. / Warwicker, J. / Winter-Holt, J. / McCoull, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72 KB | Display | ![]() |
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PDB format | ![]() | 49.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7aaxC ![]() 7aayC ![]() 7aazC ![]() 7ab0C ![]() 7ab2C ![]() 3brbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 34381.754 Da / Num. of mol.: 1 / Fragment: MERTK kinase domain / Mutation: K591R, K693R, K702R, K856R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q12866, receptor protein-tyrosine kinase | ||||||
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#2: Chemical | ChemComp-C6F / | ||||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0.1M Tris pH 8.5, 4.3M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 23, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.927→46.651 Å / Num. obs: 18953 / % possible obs: 88.3 % / Redundancy: 5.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.05 / Rrim(I) all: 0.125 / Net I/σ(I): 9.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 3BRB Resolution: 1.93→46.651 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.854 / SU ML: 0.184 / SU R Cruickshank DPI: 0.2441 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BUSTER
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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: 121.17 Å2 / Biso mean: 52.816 Å2 / Biso min: 28.03 Å2
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Refinement step | Cycle: final / Resolution: 1.93→46.651 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.977 Å / Rfactor Rfree error: 0
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