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Yorodumi- PDB-5wdy: Crystal structure of WNK1 in complex with 1-cyclohexyl-N-({6-fluo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wdy | ||||||
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Title | Crystal structure of WNK1 in complex with 1-cyclohexyl-N-({6-fluoro-1-[2-(3-methoxyphenyl)pyridin-4-yl]-1H-indol-3-yl}methyl)methanamine (compound 6) | ||||||
Components | Serine/threonine-protein kinase WNK1 | ||||||
Keywords | TRANSFERASE / kinase / inhibitor | ||||||
Function / homology | Function and homology information negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of termination of RNA polymerase II transcription / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / regulation of mRNA export from nucleus ...negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of termination of RNA polymerase II transcription / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / regulation of mRNA export from nucleus / regulation of sodium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of heterotypic cell-cell adhesion / non-membrane-bounded organelle assembly / positive regulation of T cell chemotaxis / positive regulation of systemic arterial blood pressure / potassium ion homeostasis / cellular hyperosmotic response / cellular response to chemokine / negative regulation of leukocyte cell-cell adhesion / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / negative regulation of GTPase activity / intracellular non-membrane-bounded organelle / protein kinase activator activity / sodium ion transmembrane transport / neuron development / phosphatase binding / monoatomic ion transport / regulation of sodium ion transport / negative regulation of protein ubiquitination / molecular condensate scaffold activity / negative regulation of autophagy / peptidyl-threonine phosphorylation / Stimuli-sensing channels / mitotic spindle / positive regulation of canonical Wnt signaling pathway / positive regulation of angiogenesis / heart development / T cell receptor signaling pathway / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / signal transduction / protein-containing complex / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.458 Å | ||||||
Authors | Xie, X. / Kohls, D. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models. Authors: Yamada, K. / Levell, J. / Yoon, T. / Kohls, D. / Yowe, D. / Rigel, D.F. / Imase, H. / Yuan, J. / Yasoshima, K. / DiPetrillo, K. / Monovich, L. / Xu, L. / Zhu, M. / Kato, M. / Jain, M. / ...Authors: Yamada, K. / Levell, J. / Yoon, T. / Kohls, D. / Yowe, D. / Rigel, D.F. / Imase, H. / Yuan, J. / Yasoshima, K. / DiPetrillo, K. / Monovich, L. / Xu, L. / Zhu, M. / Kato, M. / Jain, M. / Idamakanti, N. / Taslimi, P. / Kawanami, T. / Argikar, U.A. / Kunjathoor, V. / Xie, X. / Yagi, Y.I. / Iwaki, Y. / Robinson, Z. / Park, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wdy.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wdy.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/5wdy ftp://data.pdbj.org/pub/pdb/validation_reports/wd/5wdy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31893.912 Da / Num. of mol.: 2 / Fragment: UNP residues 206-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WNK1, HSN2, KDP, KIAA0344, PRKWNK1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H4A3, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: co-crystallization of protein/compound complex, reservoir solution: 100 mM Bis-Tris, pH 6.5, 20-25% PEG3350, 150-300 mM magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 25, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→50 Å / Num. obs: 17795 / % possible obs: 96.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 56.71 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.116 / Net I/σ(I): 12.5 / Num. measured all: 32987 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.458→32.843 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.44 Å2 / Biso mean: 62.6978 Å2 / Biso min: 27.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.458→32.843 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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