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- PDB-3kcf: Crystal structure of TGFbRI complexed with a pyrazolone inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kcf | ||||||
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Title | Crystal structure of TGFbRI complexed with a pyrazolone inhibitor | ||||||
![]() | TGF-beta receptor type-1 | ||||||
![]() | TRANSFERASE / KINASE / TGFBETARI / STRUCTURE-BASED DRUG DESIGN / PROTEIN-INHIBITOR COMPLEX / Aortic aneurysm / ATP-binding / Craniosynostosis / Disease mutation / Disulfide bond / Glycoprotein / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / Receptor / Serine/threonine-protein kinase / Transmembrane | ||||||
Function / homology | ![]() extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / positive regulation of tight junction disassembly / myofibroblast differentiation / 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 / positive regulation of tight junction disassembly / myofibroblast differentiation / 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 / mesenchymal cell differentiation / transforming growth factor beta receptor activity, type I / activin receptor complex / neuron fate commitment / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / receptor protein serine/threonine kinase / germ cell migration / angiogenesis involved in coronary vascular morphogenesis / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / filopodium assembly / transforming growth factor beta binding / response to cholesterol / embryonic cranial skeleton morphogenesis / I-SMAD binding / collagen fibril organization / negative regulation of chondrocyte differentiation / endothelial cell activation / skeletal system morphogenesis / endothelial cell proliferation / lens development in camera-type eye / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / SMAD binding / TGF-beta receptor signaling activates SMADs / 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 stress fiber assembly / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / negative regulation of cell migration / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / post-embryonic development / 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 / positive regulation of apoptotic signaling pathway / wound healing / cellular response to growth factor stimulus / UCH proteinases / male gonad development / 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 / Ub-specific processing proteases / regulation of cell cycle / protein kinase activity / intracellular signal transduction / endosome / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boriack-Sjodin, P.A. | ||||||
![]() | ![]() Title: Pyrazolone based TGFbetaR1 kinase inhibitors. Authors: Guckian, K. / Carter, M.B. / Lin, E.Y. / Choi, M. / Sun, L. / Boriack-Sjodin, P.A. / Chuaqui, C. / Lane, B. / Cheung, K. / Ling, L. / Lee, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 330 KB | Display | ![]() |
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PDB format | ![]() | 271.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 68.9 KB | Display | |
Data in CIF | ![]() | 90.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38920.641 Da / Num. of mol.: 5 / Fragment: UNP residues 162-503, GS AND KINASE DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36897, receptor protein serine/threonine kinase #2: Chemical | ChemComp-JZO / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Sodium potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2005 / Details: monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 73727 / Num. obs: 73525 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 52.9 Å2 / Rmerge(I) obs: 0.097 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.15 / Num. unique all: 7240 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Structure of TGFbRI with different inhibitor Resolution: 2.8→34.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3273596.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.4394 Å2 / ksol: 0.357103 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→34.86 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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