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Yorodumi- PDB-6lw2: The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lw2 | ||||||
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Title | The N-arylsulfonyl-indole-2-carboxamide-based inhibitors against fructose-1,6-bisphosphatase | ||||||
Components | Fructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase | ||||||
Keywords | HYDROLASE / FBPase / N-arylsulfonyl-indole-2-carboxamide | ||||||
Function / homology | Function and homology information 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 / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...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 / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process / fructose metabolic process / Gluconeogenesis / monosaccharide binding / negative regulation of glycolytic 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wang, X.Y. / Zhou, J. / Xu, B.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of N -Arylsulfonyl-Indole-2-Carboxamide Derivatives as Potent, Selective, and Orally Bioavailable Fructose-1,6-Bisphosphatase Inhibitors-Design, Synthesis, In Vivo Glucose Lowering ...Title: Discovery of N -Arylsulfonyl-Indole-2-Carboxamide Derivatives as Potent, Selective, and Orally Bioavailable Fructose-1,6-Bisphosphatase Inhibitors-Design, Synthesis, In Vivo Glucose Lowering Effects, and X-ray Crystal Complex Analysis. Authors: Zhou, J. / Bie, J. / Wang, X. / Liu, Q. / Li, R. / Chen, H. / Hu, J. / Cao, H. / Ji, W. / Li, Y. / Liu, S. / Shen, Z. / Xu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lw2.cif.gz | 318.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lw2.ent.gz | 208.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/6lw2 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/6lw2 | HTTPS FTP |
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-Related structure data
Related structure data | 2fieS S: Starting model for refinement |
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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: 36887.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, FBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09467, fructose-bisphosphatase #2: Chemical | ChemComp-EW0 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.66 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→140 Å / Num. obs: 65874 / % possible obs: 97.8 % / Redundancy: 2 % / Biso Wilson estimate: 36.95 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.36→6.18 Å / Num. unique obs: 80510 / CC1/2: 0.985 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FIE Resolution: 2.4→19.95 Å / SU ML: 0.3342 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8685 / Stereochemistry target values: 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: 39.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.95 Å
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Refine LS restraints |
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LS refinement shell |
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