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Yorodumi- PDB-5is5: Discovery and Pharmacological Characterization of Novel Quinazoli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5is5 | ||||||
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Title | Discovery and Pharmacological Characterization of Novel Quinazoline-based PI3K delta-selective Inhibitors | ||||||
Components | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | ||||||
Keywords | TRANSFERASE / Phosphoinositide 3-Kinase / isoform-sepcific inhibitors | ||||||
Function / homology | Function and homology information Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane / PIP3 activates AKT signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / phosphatidylinositol 3-kinase complex ...Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / Synthesis of PIPs at the plasma membrane / PIP3 activates AKT signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / B cell activation / phosphatidylinositol-mediated signaling / B cell homeostasis / homeostasis of number of cells / defense response to fungus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of angiogenesis / chemotaxis / cell migration / kinase activity / adaptive immune response / cell differentiation / cell surface receptor signaling pathway / inflammatory response / phosphorylation / negative regulation of gene expression / innate immune response / positive regulation of gene expression / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Gutmann, S. / Rummel, G. / Shrestha, B. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2016 Title: Discovery and Pharmacological Characterization of Novel Quinazoline-Based PI3K Delta-Selective Inhibitors. Authors: Hoegenauer, K. / Soldermann, N. / Stauffer, F. / Furet, P. / Graveleau, N. / Smith, A.B. / Hebach, C. / Hollingworth, G.J. / Lewis, I. / Gutmann, S. / Rummel, G. / Knapp, M. / Wolf, R.M. / ...Authors: Hoegenauer, K. / Soldermann, N. / Stauffer, F. / Furet, P. / Graveleau, N. / Smith, A.B. / Hebach, C. / Hollingworth, G.J. / Lewis, I. / Gutmann, S. / Rummel, G. / Knapp, M. / Wolf, R.M. / Blanz, J. / Feifel, R. / Burkhart, C. / Zecri, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5is5.cif.gz | 313.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5is5.ent.gz | 245.8 KB | Display | PDB format |
PDBx/mmJSON format | 5is5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5is5_validation.pdf.gz | 718.9 KB | Display | wwPDB validaton report |
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Full document | 5is5_full_validation.pdf.gz | 722.4 KB | Display | |
Data in XML | 5is5_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 5is5_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/5is5 ftp://data.pdbj.org/pub/pdb/validation_reports/is/5is5 | HTTPS FTP |
-Related structure data
Related structure data | 5itdC 2xwf 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: 119999.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pik3cd / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q3UDT3, UniProt: O35904*PLUS, phosphatidylinositol-4,5-bisphosphate 3-kinase |
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#2: Chemical | ChemComp-6CY / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 13 mM NaNO4, 13 mM ammonium sulfate, 13 mM Na2HPO4, 16.4 (v/v) % glycerol, 13 % (w/v) PEG4000, 0.1M imidazole pH6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→68.87 Å / Num. obs: 23618 / % possible obs: 97.7 % / Redundancy: 3.29 % / Rmerge(I) obs: 0.2294 / Rsym value: 0.101 / Net I/σ(I): 11.74 |
Reflection shell | Resolution: 2.61→2.68 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2xwf 2xwf Resolution: 2.85→65.95 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.85→65.95 Å
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