+Open data
-Basic information
Entry | Database: PDB / ID: 4ztm | ||||||
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Title | Irak4-inhibitor co-structure | ||||||
Components | Interleukin-1 receptor-associated kinase 4 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / KINASE / PHOSPHATASE / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information MyD88 dependent cascade initiated on endosome / IRAK4 deficiency (TLR5) / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / interleukin-1 receptor binding / neutrophil mediated immunity ...MyD88 dependent cascade initiated on endosome / IRAK4 deficiency (TLR5) / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / interleukin-1 receptor binding / neutrophil mediated immunity / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / extrinsic component of plasma membrane / JNK cascade / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / Interleukin-1 signaling / PIP3 activates AKT signaling / kinase activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / endosome membrane / intracellular signal transduction / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / cell surface / magnesium ion binding / extracellular space / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.66 Å | ||||||
Authors | Fischmann, T.O. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2015 Title: Discovery and Structure Enabled Synthesis of 2,6-Diaminopyrimidin-4-one IRAK4 Inhibitors. Authors: Seganish, W.M. / Fischmann, T.O. / Sherborne, B. / Matasi, J. / Lavey, B. / McElroy, W.T. / Tulshian, D. / Tata, J. / Sondey, C. / Garlisi, C.G. / Devito, K. / Fossetta, J. / Lundell, D. / Niu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ztm.cif.gz | 236.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ztm.ent.gz | 191.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ztm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ztm_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4ztm_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4ztm_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 4ztm_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/4ztm ftp://data.pdbj.org/pub/pdb/validation_reports/zt/4ztm | HTTPS FTP |
-Related structure data
Related structure data | 4ztlC 4ztnC 2nruS 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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Unit cell |
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-Components
#1: Protein | Mass: 33956.195 Da / Num. of mol.: 4 / Fragment: UNP residues 160-460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-4S2 / #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: 2.64 Å3/Da / Density % sol: 53.39 % / Description: Thick plates |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 1.80 to 2.0 M Sodium Malonate, 0.2 M Sodium Acetate, 25 mM Hexamminecobalt(III)chloride, 0.05%w/v Pluronic-F-68 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.66→47.321 Å / Num. all: 37506 / Num. obs: 37506 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 60.83 Å2 / Rpim(I) all: 0.048 / Rrim(I) all: 0.088 / Rsym value: 0.059 / Net I/av σ(I): 9.877 / Net I/σ(I): 13 / Num. measured all: 123255 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2NRU Resolution: 2.66→47.32 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9178 / SU R Cruickshank DPI: 2.114 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.135 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.305
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Displacement parameters | Biso max: 153.76 Å2 / Biso mean: 54.04 Å2 / Biso min: 13.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.66→47.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.73 Å / Total num. of bins used: 19
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