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Open data
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Basic information
Entry | Database: PDB / ID: 6x85 | ||||||
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Title | Crystal Structure of TNFalpha with indolinone compound 9 | ||||||
![]() | Tumor necrosis factor![]() | ||||||
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Function / homology | ![]() negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / : ...negative regulation of L-glutamate import across plasma membrane / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of neutrophil activation / negative regulation of branching involved in lung morphogenesis / positive regulation of interleukin-33 production / positive regulation of blood microparticle formation / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / : / response to macrophage colony-stimulating factor / positive regulation of vitamin D biosynthetic process / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of translational initiation by iron / response to 3,3',5-triiodo-L-thyronine / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / regulation of branching involved in salivary gland morphogenesis / chronic inflammatory response to antigenic stimulus / negative regulation of protein-containing complex disassembly / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / negative regulation of myosin-light-chain-phosphatase activity / positive regulation of hair follicle development / negative regulation of myelination / death receptor agonist activity / negative regulation of amyloid-beta clearance / negative regulation of vascular wound healing / negative regulation of bicellular tight junction assembly / response to isolation stress / negative regulation of cytokine production involved in immune response / inflammatory response to wounding / cellular response to toxic substance / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of I-kappaB phosphorylation / positive regulation of action potential / sequestering of triglyceride / TNF signaling / positive regulation of protein transport / positive regulation of interleukin-18 production / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / positive regulation of superoxide dismutase activity / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / vascular endothelial growth factor production / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / response to fructose / positive regulation of fever generation / negative regulation of myoblast differentiation / positive regulation of mononuclear cell migration / positive regulation of protein localization to cell surface / negative regulation of glucose import / TNFR1-mediated ceramide production / endothelial cell apoptotic process / regulation of establishment of endothelial barrier / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / negative regulation of oxidative phosphorylation / positive regulation of cytokine production involved in inflammatory response / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Longenecker, K.L. / Stoll, V.S. | ||||||
![]() | ![]() Title: Development of Orally Efficacious Allosteric Inhibitors of TNF alpha via Fragment-Based Drug Design. Authors: Dietrich, J.D. / Longenecker, K.L. / Wilson, N.S. / Goess, C. / Panchal, S.C. / Swann, S.L. / Petros, A.M. / Hobson, A.D. / Ihle, D. / Song, D. / Richardson, P. / Comess, K.M. / Cox, P.B. / ...Authors: Dietrich, J.D. / Longenecker, K.L. / Wilson, N.S. / Goess, C. / Panchal, S.C. / Swann, S.L. / Petros, A.M. / Hobson, A.D. / Ihle, D. / Song, D. / Richardson, P. / Comess, K.M. / Cox, P.B. / Dombrowski, A. / Sarris, K. / Donnelly-Roberts, D.L. / Duignan, D.B. / Gomtsyan, A. / Jung, P. / Krueger, A.C. / Mathieu, S. / McClure, A. / Stoll, V.S. / Wetter, J. / Mankovich, J.A. / Hajduk, P.J. / Vasudevan, A. / Stoffel, R.H. / Sun, 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 | ![]() | 174.9 KB | Display | ![]() |
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PDB format | ![]() | 138.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6x81C ![]() 6x82C ![]() 6x83C ![]() 6x86C ![]() 1tnfS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 17501.854 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-UTV / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.33 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 15% PEG 8000, 0.2M magnesium acetate, 0.05M sodium cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.691→54.026 Å / Num. obs: 24547 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 95.55 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.691→2.7 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 999 / Rrim(I) all: 0.42 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1tnf Resolution: 2.85→29.11 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.39
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Displacement parameters | Biso max: 221.4 Å2 / Biso mean: 98.71 Å2 / Biso min: 42.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→29.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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