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Yorodumi- PDB-5wex: Discovery of new selenoureido analogs of 4-(4-fluorophenylureido)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wex | ||||||
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Title | Discovery of new selenoureido analogs of 4-(4-fluorophenylureido) benzenesulfonamides as carbonic anhydrase inhibitors | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / Carbonic Anhydrase Inhibitors / Metalloenzymes / Glutathione Peroxidase / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.26 Å | ||||||
Authors | Angeli, A. / Tanini, D. / Peat, T.S. / Di Cesare Mannelli, L. / Bartolucci, G. / Capperucci, A. / Ghelardini, C. / Supuran, C.T. / Carta, F. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Discovery of New Selenoureido Analogues of 4-(4-Fluorophenylureido)benzenesulfonamide as Carbonic Anhydrase Inhibitors. Authors: Angeli, A. / Tanini, D. / Peat, T.S. / Di Cesare Mannelli, L. / Bartolucci, G. / Capperucci, A. / Ghelardini, C. / Supuran, C.T. / Carta, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wex.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wex.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/5wex ftp://data.pdbj.org/pub/pdb/validation_reports/we/5wex | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 241 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-8JS / |
#5: Chemical | ChemComp-DMS / |
#6: 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: 2.11 Å3/Da / Density % sol: 41.67 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: concentrated CA II at about 10 mg/mL was set up in SD-2 plates with the following ratio of protein plus reservoir plus seeds: 250nL plus 225 nL plus 25 nL. The plate was incubated at 8C and ...Details: concentrated CA II at about 10 mg/mL was set up in SD-2 plates with the following ratio of protein plus reservoir plus seeds: 250nL plus 225 nL plus 25 nL. The plate was incubated at 8C and the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8. 3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→41.1 Å / Num. obs: 63929 / % possible obs: 96.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rsym value: 0.089 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 6 % / Rmerge(I) obs: 1.175 / Mean I/σ(I) obs: 2 / Num. unique obs: 3012 / CC1/2: 0.609 / Rpim(I) all: 0.511 / Rsym value: 1.286 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Resolution: 1.26→41.1 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.297 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.971 Å2
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Refinement step | Cycle: 1 / Resolution: 1.26→41.1 Å
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