+Open data
-Basic information
Entry | Database: PDB / ID: 2qbq | ||||||
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Title | Crystal structure of ptp1b-inhibitor complex | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 1 | ||||||
Keywords | HYDROLASE / PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane ...regulation of hepatocyte growth factor receptor signaling pathway / PTK6 Down-Regulation / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / positive regulation of receptor catabolic process / insulin receptor recycling / negative regulation of PERK-mediated unfolded protein response / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of intracellular protein transport / IRE1-mediated unfolded protein response / cytoplasmic side of endoplasmic reticulum membrane / platelet-derived growth factor receptor-beta signaling pathway / sorting endosome / mitochondrial crista / positive regulation of IRE1-mediated unfolded protein response / regulation of type I interferon-mediated signaling pathway / regulation of endocytosis / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of protein tyrosine kinase activity / peptidyl-tyrosine dephosphorylation / Regulation of IFNA/IFNB signaling / regulation of signal transduction / cellular response to unfolded protein / 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 / positive regulation of JUN kinase activity / Insulin receptor recycling / negative regulation of insulin receptor signaling pathway / ephrin receptor binding / Integrin signaling / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / protein phosphatase 2A binding / protein tyrosine phosphatase activity / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Xu, W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Structure-based optimization of protein tyrosine phosphatase 1B inhibitors: from the active site to the second phosphotyrosine binding site. Authors: Wilson, D.P. / Wan, Z.K. / Xu, W.X. / Kirincich, S.J. / Follows, B.C. / Joseph-McCarthy, D. / Foreman, K. / Moretto, A. / Wu, J. / Zhu, M. / Binnun, E. / Zhang, Y.L. / Tam, M. / Erbe, D.V. / ...Authors: Wilson, D.P. / Wan, Z.K. / Xu, W.X. / Kirincich, S.J. / Follows, B.C. / Joseph-McCarthy, D. / Foreman, K. / Moretto, A. / Wu, J. / Zhu, M. / Binnun, E. / Zhang, Y.L. / Tam, M. / Erbe, D.V. / Tobin, J. / Xu, X. / Leung, L. / Shilling, A. / Tam, S.Y. / Mansour, T.S. / Lee, J. #1: Journal: Bioorg.Med.Chem. / Year: 2006 Title: Bicyclic and Tricyclic Thiophenes as Protein Tyrosine Phosphatase 1B Inhibitor Authors: Moretto, A.F. / Kirincich, S.J. / Xu, W.X. / Smith, M.J. / Wan, Z.-K. / Wilson, D.P. / Follows, B.C. / Binnun, E. / Joseph-Mccarthy, D. / Foreman, K. / Erbe, D.V. / Zhang, Y.-L. / Tam, S.K. / Tam, S.Y. / Lee, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qbq.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qbq.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qbq_validation.pdf.gz | 768.1 KB | Display | wwPDB validaton report |
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Full document | 2qbq_full_validation.pdf.gz | 772.3 KB | Display | |
Data in XML | 2qbq_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 2qbq_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/2qbq ftp://data.pdbj.org/pub/pdb/validation_reports/qb/2qbq | HTTPS FTP |
-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: 34833.723 Da / Num. of mol.: 1 Fragment: Tyrosine-protein phosphatase domain, CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN1, PTP1B / Production host: Escherichia coli (E. coli) / References: UniProt: P18031, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-4B3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.49 % |
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Crystal grow | pH: 7 Details: 17% PEG 4000, 0.15M MGCL2, 0.1M HEPES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 17, 2002 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 27473 / % possible obs: 98.4 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.1→2.13 Å / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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