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- PDB-7cvn: The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cvn | ||||||
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Title | The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against fructose-1,6-bisphosphatase | ||||||
![]() | Fructose-1,6-bisphosphatase 1 | ||||||
![]() | HYDROLASE / Fructose-1 / 6-bisphosphatase / N-arylsulfonyl-indole-2-carboxamide | ||||||
Function / homology | ![]() cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / monosaccharide binding / negative regulation of glycolytic process / fructose 1,6-bisphosphate metabolic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, X. / Zhou, J. / Xu, B. | ||||||
![]() | ![]() Title: Design,synthesis,biological evaluation and binding mode analysis of 7-nitro-indole-N-acylarylsulfonamide-based fructose-1,6-bisphosphatase inhibitors Authors: Bie, J. / Wang, X. / Liu, S. / Zhou, J. / Liu, Q. / Shen, Z. / Xu, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321 KB | Display | ![]() |
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PDB format | ![]() | 209.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 51.2 KB | Display | |
Data in CIF | ![]() | 69.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fieS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36887.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GJO / #3: Sugar | ChemComp-FBP / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M Ammonium acetate, 0.1M HEPES, 20% PEG 3350, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→92.71 Å / Num. obs: 41781 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 17.85 Å2 / CC1/2: 0.971 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.75→2.86 Å / Num. unique obs: 49738 / CC1/2: 0.914 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FIE Resolution: 2.75→21.52 Å / SU ML: 0.2577 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8378 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→21.52 Å
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Refine LS restraints |
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LS refinement shell |
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