+Open data
-Basic information
Entry | Database: PDB / ID: 4ivd | ||||||
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Title | JAK1 kinase (JH1 domain) in complex with compound 34 | ||||||
Components | Tyrosine-protein kinase JAK1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN KINASE / PHOSPHO TRANSFER / PHOSPHO TYROSINE / TRANSFERASE- TRANSFERASE INHIBITOR COMPLEX / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / type III interferon-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway ...protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / type III interferon-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of homotypic cell-cell adhesion / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-2 signaling / growth hormone receptor binding / Other interleukin signaling / IFNG signaling activates MAPKs / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / type I interferon-mediated signaling pathway / Interleukin-6 signaling / positive regulation of sprouting angiogenesis / MAPK3 (ERK1) activation / Interleukin-10 signaling / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Signaling by CSF3 (G-CSF) / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / Evasion by RSV of host interferon responses / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / ISG15 antiviral mechanism / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / Interferon gamma signaling / Interferon alpha/beta signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / cytoskeleton / endosome / intracellular signal transduction / protein phosphorylation / response to antibiotic / focal adhesion / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Eigenbrot, C. / Steffek, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Identification of C-2 Hydroxyethyl Imidazopyrrolopyridines as Potent JAK1 Inhibitors with Favorable Physicochemical Properties and High Selectivity over JAK2. Authors: Zak, M. / Hurley, C.A. / Ward, S.I. / Bergeron, P. / Barrett, K. / Balazs, M. / Blair, W.S. / Bull, R. / Chakravarty, P. / Chang, C. / Crackett, P. / Deshmukh, G. / Devoss, J. / Dragovich, P. ...Authors: Zak, M. / Hurley, C.A. / Ward, S.I. / Bergeron, P. / Barrett, K. / Balazs, M. / Blair, W.S. / Bull, R. / Chakravarty, P. / Chang, C. / Crackett, P. / Deshmukh, G. / Devoss, J. / Dragovich, P.S. / Eigenbrot, C. / Ellwood, C. / Gaines, S. / Ghilardi, N. / Gibbons, P. / Gradl, S. / Gribling, P. / Hamman, C. / Harstad, E. / Hewitt, P. / Johnson, A. / Johnson, T. / Kenny, J.R. / Koehler, M.F. / Bir Kohli, P. / Labadie, S. / Lee, W.P. / Liao, J. / Liimatta, M. / Mendonca, R. / Narukulla, R. / Pulk, R. / Reeve, A. / Savage, S. / Shia, S. / Steffek, M. / Ubhayakar, S. / van Abbema, A. / Aliagas, I. / Avitabile-Woo, B. / Xiao, Y. / Yang, J. / Kulagowski, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ivd.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ivd.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ivd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/4ivd ftp://data.pdbj.org/pub/pdb/validation_reports/iv/4ivd | HTTPS FTP |
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-Related structure data
Related structure data | 4ivaC 4ivbC 4ivcC 4fk6S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34746.594 Da / Num. of mol.: 2 / Fragment: UNP residues 854-1154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JAK1, JAK1A, JAK1B / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P23458, non-specific protein-tyrosine kinase #2: Chemical | #3: 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: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: MES/PEG6000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 48323 / Num. obs: 48317 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.098 / Net I/σ(I): 12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FK6 Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.39 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.242 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2.034 Å / Total num. of bins used: 10
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