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Yorodumi- PDB-2cnh: Structural Insights into the Design of Nonpeptidic Isothiazolidin... -
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-Basic information
Entry | Database: PDB / ID: 2cnh | ||||||
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Title | Structural Insights into the Design of Nonpeptidic Isothiazolidinone- Containing Inhibitors of Protein Tyrosine Phosphatase 1B | ||||||
Components | TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1 | ||||||
Keywords | HYDROLASE / POLYMORPHISM / PHOSPHORYLATION / PROTEIN PHOSPHATASE / ENDOPLASMIC RETICULUM / OXIDATION / ACETYLATION / PHOSPHATASE | ||||||
Function / homology | Function and homology information PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport ...PTK6 Down-Regulation / regulation of hepatocyte growth factor receptor signaling pathway / positive regulation of receptor catabolic process / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / insulin receptor recycling / negative regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of IRE1-mediated unfolded protein response / negative regulation of PERK-mediated unfolded protein response / IRE1-mediated unfolded protein response / regulation of intracellular protein transport / cytoplasmic side of endoplasmic reticulum membrane / sorting endosome / mitochondrial crista / platelet-derived growth factor receptor-beta signaling pathway / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / positive regulation of protein tyrosine kinase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / cellular response to unfolded protein / regulation of signal transduction / growth hormone receptor signaling pathway via JAK-STAT / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of signal transduction / Regulation of IFNG signaling / MECP2 regulates neuronal receptors and channels / Growth hormone receptor signaling / endoplasmic reticulum unfolded protein response / negative regulation of MAP kinase activity / positive regulation of JUN kinase activity / negative regulation of insulin receptor signaling pathway / Insulin receptor recycling / ephrin receptor binding / protein dephosphorylation / Integrin signaling / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein phosphatase 2A binding / endosome lumen / insulin receptor binding / Negative regulation of MET activity / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / insulin receptor signaling pathway / actin cytoskeleton organization / early endosome / mitochondrial matrix / cadherin binding / protein kinase binding / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ala, P.J. / Gonneville, L. / Hillman, M. / Becker-Pasha, M. / Yue, E.W. / Douty, B. / Wayland, B. / Polam, P. / Crawley, M.L. / McLaughlin, E. ...Ala, P.J. / Gonneville, L. / Hillman, M. / Becker-Pasha, M. / Yue, E.W. / Douty, B. / Wayland, B. / Polam, P. / Crawley, M.L. / McLaughlin, E. / Sparks, R.B. / Glass, B. / Takvorian, A. / Combs, A.P. / Burn, T.C. / Hollis, G.F. / Wynn, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural Insights Into the Design of Nonpeptidic Isothiazolidinone-Containing Inhibitors of Protein- Tyrosine Phosphatase 1B. Authors: Ala, P.J. / Gonneville, L. / Hillman, M. / Becker-Pasha, M. / Yue, E.W. / Douty, B. / Wayland, B. / Polam, P. / Crawley, M.L. / Mclaughlin, E. / Sparks, R.B. / Glass, B. / Takvorian, A. / ...Authors: Ala, P.J. / Gonneville, L. / Hillman, M. / Becker-Pasha, M. / Yue, E.W. / Douty, B. / Wayland, B. / Polam, P. / Crawley, M.L. / Mclaughlin, E. / Sparks, R.B. / Glass, B. / Takvorian, A. / Combs, A.P. / Burn, T.C. / Hollis, G.F. / Wynn, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cnh.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cnh.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cnh_validation.pdf.gz | 457.1 KB | Display | wwPDB validaton report |
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Full document | 2cnh_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 2cnh_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 2cnh_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/2cnh ftp://data.pdbj.org/pub/pdb/validation_reports/cn/2cnh | HTTPS FTP |
-Related structure data
Related structure data | 2cneC 2cnfC 2cngC 2cniC 1eeoS 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: 37365.637 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-IZB / |
#4: Water | ChemComp-HOH / |
Compound details | MAY PLAY AN IMPORTANT ROLE IN CKII- AND P60C-SRC-INDUCED SIGNAL TRANSDUCTI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.06 % |
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Crystal grow | pH: 7.3 / Details: 160 MM CALCIUM ACETATE, PH 7.3, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU MSC RAXIS IV / Detector: IMAGE PLATE / Details: BLUE CONFOCAL MAX-FLUX 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: 1.8→19.9 Å / Num. obs: 38984 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4 / % possible all: 97.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EEO Resolution: 1.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Bsol: 280 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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