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Yorodumi- PDB-2wot: ALK5 IN COMPLEX WITH 4-((5,6-dimethyl-2-(2-pyridyl)-3-pyridyl)oxy... -
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-Basic information
Entry | Database: PDB / ID: 2wot | ||||||
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Title | ALK5 IN COMPLEX WITH 4-((5,6-dimethyl-2-(2-pyridyl)-3-pyridyl)oxy)-N-(3,4,5-trimethoxyphenyl)pyridin-2-amine | ||||||
Components | TGF-BETA RECEPTOR TYPE-1 | ||||||
Keywords | TRANSFERASE / ALK5 / KINASE / MEMBRANE / RECEPTOR / MANGANESE / SERINE/THREONINE-PROTEIN KINASE / KINASE INHIBITOR / DISEASE MUTATION / CRANIOSYNOSTOSIS / NUCLEOTIDE-BINDING / TGF BETA TYPE I RECEPTOR / PHOSPHOPROTEIN / DISULFIDE BOND / AORTIC ANEURYSM / GLYCOPROTEIN / METAL-BINDING / TRANSMEMBRANE / ATP-BINDING | ||||||
Function / homology | Function and homology information extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity ...extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / activin receptor activity, type I / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / neuron fate commitment / germ cell migration / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / filopodium assembly / ventricular trabecula myocardium morphogenesis / transforming growth factor beta binding / embryonic cranial skeleton morphogenesis / response to cholesterol / I-SMAD binding / negative regulation of chondrocyte differentiation / collagen fibril organization / endothelial cell proliferation / endothelial cell activation / skeletal system morphogenesis / lens development in camera-type eye / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / TGF-beta receptor signaling activates SMADs / SMAD binding / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / endothelial cell migration / bicellular tight junction / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of apoptotic signaling pathway / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / Downregulation of TGF-beta receptor signaling / post-embryonic development / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / thymus development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / skeletal system development / cell motility / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cellular response to growth factor stimulus / male gonad development / UCH proteinases / nervous system development / heart development / positive regulation of cell growth / regulation of gene expression / peptidyl-serine phosphorylation / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / regulation of cell cycle / Ub-specific processing proteases / endosome / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Norman, R.A. / Debreczeni, J.E. / Goldberg, F.W. / Ward, R.A. / Finlay, R. / Powell, S.J. / Roberts, N.J. / Dishington, A.P. / Gingell, H.J. / Wickson, K.F. / Roberts, A.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Rapid Generation of a High Quality Lead for Transforming Growth Factor-Beta (Tgf-Beta) Type I Receptor (Alk5). Authors: Goldberg, F.W. / Ward, R.A. / Powell, S.J. / Debreczeni, J.E. / Norman, R.A. / Roberts, N.J. / Dishington, A.P. / Gingell, H.J. / Wickson, K.F. / Roberts, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wot.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wot.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 2wot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wot ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wot | HTTPS FTP |
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-Related 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: 34939.199 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 200-503 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: P36897, receptor protein serine/threonine kinase |
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#2: Chemical | ChemComp-ZZG / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Sequence details | G198 AND G199 ARE CLONING ARTIFACTS. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.36 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop Details: SITTING DROP METHOD. DROPS PROTEIN-PRECIPITANT 1-1, PROTEIN: 10MG/ML ALK5, PRECIPITANT: 20-30% PEG8K, 100 MM PCTP BUFFER PH 8.5-9.2, 0.2 M NAAC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 24, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→22.5 Å / Num. obs: 25080 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.53 % / Biso Wilson estimate: 11.289 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.98 / % possible all: 87.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→22.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.013 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.142 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.258 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→22.27 Å
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