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Yorodumi- PDB-2wqb: Structure of the Tie2 kinase domain in complex with a thiazolopyr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wqb | ||||||
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Title | Structure of the Tie2 kinase domain in complex with a thiazolopyrimidine inhibitor | ||||||
Components | ANGIOPOIETIN-1 RECEPTOR | ||||||
Keywords | TRANSFERASE / PHOSPHOPROTEIN / KINASE / RECEPTOR / ONCOLOGY / ATP-BINDING / GLYCOPROTEIN / TYROSINE-PROTEIN KINASE / PHOSPHOTRANSFERASE / NUCLEOTIDE-BINDING / DISEASE MUTATION / THIAZOLOPYRIMIDINE | ||||||
Function / homology | Function and homology information Tie signaling pathway / glomerulus vasculature development / regulation of establishment or maintenance of cell polarity / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / positive regulation of intracellular signal transduction / sprouting angiogenesis ...Tie signaling pathway / glomerulus vasculature development / regulation of establishment or maintenance of cell polarity / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / positive regulation of intracellular signal transduction / sprouting angiogenesis / endothelial cell proliferation / positive regulation of Rho protein signal transduction / growth factor binding / positive regulation of Rac protein signal transduction / positive regulation of focal adhesion assembly / microvillus / centriolar satellite / negative regulation of endothelial cell apoptotic process / cell surface receptor protein tyrosine kinase signaling pathway / Tie2 Signaling / response to cAMP / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / negative regulation of angiogenesis / basal plasma membrane / receptor protein-tyrosine kinase / response to peptide hormone / negative regulation of inflammatory response / response to estrogen / positive regulation of angiogenesis / cell-cell junction / cell-cell signaling / signaling receptor activity / heart development / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / response to hypoxia / protein kinase activity / positive regulation of protein phosphorylation / apical plasma membrane / membrane raft / focal adhesion / negative regulation of apoptotic process / cell surface / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Brassington, C. / Breed, J. / Buttar, D. / Fitzek, M. / Forder, C. / Hassall, L. / Hayter, B.R. / Jones, C.D. / Luke, R.W.A. / McCall, E. ...Brassington, C. / Breed, J. / Buttar, D. / Fitzek, M. / Forder, C. / Hassall, L. / Hayter, B.R. / Jones, C.D. / Luke, R.W.A. / McCall, E. / McCoull, W. / Norman, R. / Paterson, D. / McMiken, H. / Rowsell, S. / Tucker, J.A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Novel Thienopyrimidine and Thiazolopyrimidine Kinase Inhibitors with Activity Against Tie-2 in Vitro and in Vivo. Authors: Luke, R.W. / Ballard, P. / Buttar, D. / Campbell, L. / Curwen, J. / Emery, S.C. / Griffen, A.M. / Hassall, L. / Hayter, B.R. / Jones, C.D. / Mccoull, W. / Mellor, M. / Swain, M.L. / Tucker, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wqb.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wqb.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 2wqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wqb_validation.pdf.gz | 804.1 KB | Display | wwPDB validaton report |
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Full document | 2wqb_full_validation.pdf.gz | 808.9 KB | Display | |
Data in XML | 2wqb_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2wqb_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/2wqb ftp://data.pdbj.org/pub/pdb/validation_reports/wq/2wqb | HTTPS FTP |
-Related structure data
Related structure data | 1fvrS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36993.234 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 802-1124 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 References: UniProt: Q02763, receptor protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-QQ1 / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | MUTATION AT D964N TO RENDER EXPRESSED PROTEIN KINASE DEAD. ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 5 MG/ML PROTEIN, 5% (W/V) PEG6000, 5% (V/V) MPD, 100MM MOPS PH7.5, 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 19, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→32.97 Å / Num. obs: 9451 / % possible obs: 98.3 % / Observed criterion σ(I): 3.7 / Redundancy: 5.3 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.78 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FVR Resolution: 2.95→32.97 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 32.445 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.362 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→32.97 Å
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Refine LS restraints |
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