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- PDB-6yr9: FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yr9 | ||||||
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Title | FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N-(2-{[2-(2-oxo-2,3-dihydro-1H-indol-5-ylamino)-5-trifluoromethyl-pyrimidin-4-ylamino]-methyl}-phenyl)-methanesulfonamide | ||||||
![]() | Focal adhesion kinase 1 | ||||||
![]() | TRANSFERASE / PROTEIN TYROSINE KINASE / ATP BINDING / TRANSFERASE-INHIBITOR COMPLEX | ||||||
Function / homology | ![]() netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of fibroblast migration / positive regulation of macrophage proliferation ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of fibroblast migration / positive regulation of macrophage proliferation / DCC mediated attractive signaling / growth hormone receptor signaling pathway / Signal regulatory protein family interactions / regulation of osteoblast differentiation / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / regulation of GTPase activity / negative regulation of cell-cell adhesion / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / positive regulation of macrophage chemotaxis / positive regulation of epithelial cell migration / regulation of cytoskeleton organization / Apoptotic cleavage of cellular proteins / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ephrin receptor signaling pathway / positive regulation of protein kinase activity / RHO GTPases Activate WASPs and WAVEs / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / Integrin signaling / SH2 domain binding / transforming growth factor beta receptor signaling pathway / ciliary basal body / protein tyrosine phosphatase activity / molecular function activator activity / axon guidance / integrin-mediated signaling pathway / cell motility / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / regulation of protein phosphorylation / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / placenta development / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / integrin binding / cell migration / actin binding / regulation of cell population proliferation / regulation of cell shape / cell cortex / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / angiogenesis / protein autophosphorylation / Extra-nuclear estrogen signaling / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / focal adhesion / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Musil, D. / Amaral, M. | ||||||
![]() | ![]() Title: Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2. Authors: Berger, B.T. / Amaral, M. / Kokh, D.B. / Nunes-Alves, A. / Musil, D. / Heinrich, T. / Schroder, M. / Neil, R. / Wang, J. / Navratilova, I. / Bomke, J. / Elkins, J.M. / Muller, S. / Frech, M. ...Authors: Berger, B.T. / Amaral, M. / Kokh, D.B. / Nunes-Alves, A. / Musil, D. / Heinrich, T. / Schroder, M. / Neil, R. / Wang, J. / Navratilova, I. / Bomke, J. / Elkins, J.M. / Muller, S. / Frech, M. / Wade, R.C. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 434.4 KB | Display | ![]() |
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PDB format | ![]() | 361 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yojC ![]() 6yq1C ![]() 6yt6C ![]() 6yvsC ![]() 6yvyC ![]() 6yxvC ![]() 4gu6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32304.221 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q05397, non-specific protein-tyrosine kinase #2: Chemical | ChemComp-P9K / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15% PEG 3350, 0.2 M Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99993 Å / Relative weight: 1 |
Reflection | Resolution: 1.925→84.03 Å / Num. obs: 48069 / % possible obs: 88 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rpim(I) all: 0.045 / Rrim(I) all: 0.063 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.925→2.168 Å / Num. unique obs: 2402 / CC1/2: 0.67 / Rrim(I) all: 0.771 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GU6 Resolution: 1.925→84.03 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.365 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.23
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Displacement parameters | Biso max: 104.33 Å2 / Biso mean: 38.36 Å2 / Biso min: 7.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.925→84.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2.09 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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