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Yorodumi- PDB-7q6h: HUMAN JAK3 KINASE DOMAIN WITH 1-(4-((2-((1-methyl-1H-pyrazol-4-yl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q6h | ||||||
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Title | HUMAN JAK3 KINASE DOMAIN WITH 1-(4-((2-((1-methyl-1H-pyrazol-4-yl)amino)quinazolin-8-yl)amino)piperidin-1-yl)ethan-1-one | ||||||
Components | Tyrosine-protein kinase JAK3 | ||||||
Keywords | SIGNALING PROTEIN / INHIBITOR / JAK3 / KINASE | ||||||
Function / homology | Function and homology information negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling ...negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / regulation of T cell apoptotic process / negative regulation of interleukin-12 production / interleukin-15-mediated signaling pathway / tyrosine phosphorylation of STAT protein / negative regulation of thymocyte apoptotic process / Interleukin-15 signaling / Interleukin-2 signaling / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / Signaling by ALK / extrinsic component of plasma membrane / Interleukin-20 family signaling / negative regulation of interleukin-10 production / enzyme-linked receptor protein signaling pathway / T cell homeostasis / cell surface receptor signaling pathway via JAK-STAT / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / B cell differentiation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / RAF/MAP kinase cascade / regulation of apoptotic process / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / cell differentiation / cytoskeleton / intracellular signal transduction / endosome / protein phosphorylation / innate immune response / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å | ||||||
Authors | Chung, C. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Investigation of Janus Kinase (JAK) Inhibitors for Lung Delivery and the Importance of Aldehyde Oxidase Metabolism. Authors: Wellaway, C.R. / Baldwin, I.R. / Bamborough, P. / Barker, D. / Bartholomew, M.A. / Chung, C.W. / Dumpelfeld, B. / Evans, J.P. / Fazakerley, N.J. / Homes, P. / Keeling, S.P. / Lewell, X.Q. / ...Authors: Wellaway, C.R. / Baldwin, I.R. / Bamborough, P. / Barker, D. / Bartholomew, M.A. / Chung, C.W. / Dumpelfeld, B. / Evans, J.P. / Fazakerley, N.J. / Homes, P. / Keeling, S.P. / Lewell, X.Q. / McNab, F.W. / Morley, J. / Needham, D. / Neu, M. / van Oosterhout, A.J.M. / Pal, A. / Reinhard, F.B.M. / Rianjongdee, F. / Robertson, C.M. / Rowland, P. / Shah, R.R. / Sherriff, E.B. / Sloan, L.A. / Teague, S. / Thomas, D.A. / Wellaway, N. / Wojno-Picon, J. / Woolven, J.M. / Coe, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q6h.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q6h.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q6h_validation.pdf.gz | 801.1 KB | Display | wwPDB validaton report |
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Full document | 7q6h_full_validation.pdf.gz | 802.2 KB | Display | |
Data in XML | 7q6h_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 7q6h_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/7q6h ftp://data.pdbj.org/pub/pdb/validation_reports/q6/7q6h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37177.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JAK3 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P52333, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-934 / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-PHU / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 8-20% PEG3350 and 0.2-0.3M ammonium sulphate (AS). 2% phenylurea |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.749→89.45 Å / Num. obs: 32901 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.75→1.87 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5836 / CC1/2: 0.848 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house Resolution: 1.749→57.581 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.547 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.117 Details: Hydrogens have been added in their riding positions
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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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.526 Å2
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Refinement step | Cycle: LAST / Resolution: 1.749→57.581 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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