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Yorodumi- PDB-4i6q: JAK3 kinase domain in complex with 2-Phenoxy-5H-pyrrolo[2,3-b]pyr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i6q | ||||||
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Title | JAK3 kinase domain in complex with 2-Phenoxy-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid ((S)-1-cyclopropyl-ethyl)-amide | ||||||
Components | Tyrosine-protein kinase JAK3 | ||||||
Keywords | Transferase/Transferase Inhibitor / Kinase-Inhibitor Complex / Transferase-Transferase Inhibitor complex | ||||||
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 / negative regulation of T-helper 17 cell lineage commitment / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / interleukin-7-mediated signaling pathway / Interleukin-9 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 / negative regulation of T-helper 17 cell lineage commitment / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / interleukin-7-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / negative regulation of T cell activation / interleukin-4-mediated signaling pathway / regulation of T cell apoptotic process / interleukin-2-mediated signaling pathway / negative regulation of interleukin-12 production / tyrosine phosphorylation of STAT protein / interleukin-15-mediated signaling pathway / negative regulation of thymocyte apoptotic process / Interleukin-15 signaling / Interleukin-2 signaling / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / extrinsic component of plasma membrane / Signaling by ALK / Interleukin-20 family signaling / negative regulation of interleukin-10 production / enzyme-linked receptor protein signaling pathway / T cell homeostasis / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor signaling pathway via JAK-STAT / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / 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 / cytoplasmic side of plasma membrane / RAF/MAP kinase cascade / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / protein phosphatase binding / regulation of apoptotic process / 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 / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Kuglstatter, A. / Shao, A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Discovery of a series of novel 5H-pyrrolo[2,3-b]pyrazine-2-phenyl ethers, as potent JAK3 kinase inhibitors. Authors: Jaime-Figueroa, S. / De Vicente, J. / Hermann, J. / Jahangir, A. / Jin, S. / Kuglstatter, A. / Lynch, S.M. / Menke, J. / Niu, L. / Patel, V. / Shao, A. / Soth, M. / Vu, M.D. / Yee, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i6q.cif.gz | 130 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i6q.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 4i6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i6q_validation.pdf.gz | 864.3 KB | Display | wwPDB validaton report |
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Full document | 4i6q_full_validation.pdf.gz | 866.1 KB | Display | |
Data in XML | 4i6q_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 4i6q_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6q ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6q | HTTPS FTP |
-Related structure data
Related structure data | 3zepC 4hvdS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 35613.598 Da / Num. of mol.: 1 / Fragment: RESIDUES 811-1124, PROTEIN KINASE DOMAIN / Mutation: C1040S, C1048S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JAK3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P52333, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-PHU / |
#3: Chemical | ChemComp-1DT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG3350, 0.1M MES, 0.2M MgCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→41.54 Å / Num. obs: 25796 / % possible obs: 97.66 % / Redundancy: 5.4 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.084 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.85→1.93 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.483 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 4HVD Resolution: 1.85→41.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.431 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 37.798 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→41.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.0738 Å / Origin y: -13.7315 Å / Origin z: -14.9193 Å
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