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- PDB-6nzf: CRYSTAL STRUCTURE OF TYROSINE KINASE 2 JH2 (PSEUDO KINASE DOMAIN)... -
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Basic information
Entry | Database: PDB / ID: 6nzf | ||||||
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Title | CRYSTAL STRUCTURE OF TYROSINE KINASE 2 JH2 (PSEUDO KINASE DOMAIN) COMPLEXED WITH Compound_5 AKA 4-[(2-CARBAMOYLPHEN YL)AMINO]-6-[(5-FLUOROPYRIDIN-2-YL)AMINO]-N-METHYLPYRIDINE -3-CARBOXAMIDE | ||||||
![]() | Non-receptor tyrosine-protein kinase TYK2 | ||||||
![]() | TRANSFERASE / JTK1 | ||||||
Function / homology | ![]() type III interferon-mediated signaling pathway / interleukin-10-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling ...type III interferon-mediated signaling pathway / interleukin-10-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / positive regulation of natural killer cell proliferation / growth hormone receptor binding / Other interleukin signaling / extrinsic component of plasma membrane / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / MAPK3 (ERK1) activation / positive regulation of interleukin-17 production / Interleukin-10 signaling / extrinsic component of cytoplasmic side of plasma membrane / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / type II interferon-mediated signaling pathway / positive regulation of T cell proliferation / Signaling by CSF3 (G-CSF) / non-specific protein-tyrosine kinase / positive regulation of receptor signaling pathway via JAK-STAT / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / cytoplasmic side of plasma membrane / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / positive regulation of type II interferon production / Interferon alpha/beta signaling / Signaling by ALK fusions and activated point mutants / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / cytoskeleton / intracellular signal transduction / immune response / protein phosphorylation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular exosome / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Muckelbauer, J.M. | ||||||
![]() | ![]() Title: Identification ofN-Methyl Nicotinamide andN-Methyl Pyridazine-3-Carboxamide Pseudokinase Domain Ligands as Highly Selective Allosteric Inhibitors of Tyrosine Kinase 2 (TYK2). Authors: Moslin, R. / Zhang, Y. / Wrobleski, S.T. / Lin, S. / Mertzman, M. / Spergel, S. / Tokarski, J.S. / Strnad, J. / Gillooly, K. / McIntyre, K.W. / Zupa-Fernandez, A. / Cheng, L. / Sun, H. / ...Authors: Moslin, R. / Zhang, Y. / Wrobleski, S.T. / Lin, S. / Mertzman, M. / Spergel, S. / Tokarski, J.S. / Strnad, J. / Gillooly, K. / McIntyre, K.W. / Zupa-Fernandez, A. / Cheng, L. / Sun, H. / Chaudhry, C. / Huang, C. / D'Arienzo, C. / Heimrich, E. / Yang, X. / Muckelbauer, J.K. / Chang, C. / Tredup, J. / Mulligan, D. / Xie, D. / Aranibar, N. / Chiney, M. / Burke, J.R. / Lombardo, L. / Carter, P.H. / Weinstein, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.8 KB | Display | ![]() |
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PDB format | ![]() | 84 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6nzeC ![]() 6nzhC ![]() 4wovS 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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Unit cell |
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Components
#1: Protein | Mass: 35499.156 Da / Num. of mol.: 2 / Fragment: Pseudo kinase domain, residues 575-869 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P29597, non-specific protein-tyrosine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200 mM ammonium sulfate, and 100 mM HEPES buffer, pH 7.5, 30%(W/V) PEG 5000 (Methyl Ether) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→46.29 Å / Num. obs: 25218 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 56.73 Å2 / Rsym value: 0.054 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 7.55→46.29 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 39.3 / Rsym value: 0.02 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WOV Resolution: 2.39→46.29 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.899 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.214
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Displacement parameters | Biso max: 125.85 Å2 / Biso mean: 51.05 Å2 / Biso min: 30.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.39→46.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
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