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Yorodumi- PDB-6ceh: Design, Synthesis, X-ray and Biological Activities of Selenides B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ceh | ||||||
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Title | Design, Synthesis, X-ray and Biological Activities of Selenides Bearing the Benzenesulfonamide Moiety as New Class of Agents for Prevention of Diabetic Cerebrovascular Pathology | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / Carbonic Anhydrase Inhibitors / diabetic pathology / organoselenium / 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 / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Peat, T.S. / Angeli, A. / di Cesare Mannelli, L. / Trallori, E. / Ghelardini, C. / Carta, F. / Supuran, C.T. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2018 Title: Design, Synthesis, and X-ray of Selenides as New Class of Agents for Prevention of Diabetic Cerebrovascular Pathology. Authors: Angeli, A. / di Cesare Mannelli, L. / Trallori, E. / Peat, T.S. / Ghelardini, C. / Carta, F. / Supuran, C.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ceh.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ceh.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ceh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/6ceh ftp://data.pdbj.org/pub/pdb/validation_reports/ce/6ceh | HTTPS FTP |
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-Related structure data
Related structure data | 4cq0S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29157.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pACA / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 377 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | #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: 41.68 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 200 nL 7 mg/mL protein + 200 nL reservoir solution (2.9 M ammonium sulfate, 100 mM Tris buffer, pH 8.3), equilibriated at 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 6, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→41.5 Å / Num. obs: 45001 / % possible obs: 99.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.43→1.46 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CQ0 Resolution: 1.43→41.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.384 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.074 / 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: 11.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→41.5 Å
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Refine LS restraints |
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