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Yorodumi- PDB-6oe1: Benzensulfonamides bearing spyrohydantoin moieties act as potent ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oe1 | ||||||
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Title | Benzensulfonamides bearing spyrohydantoin moieties act as potent inhibitors of human carbonic anhydrases II and VII and show neuropathic pain attenuating effects | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / carbonic anhydrase inhibitors / metalloenzymes / 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 / morphogenesis of an epithelium / regulation of intracellular pH / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Peat, T.S. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Benzensulfonamides bearing spyrohydantoin moieties act as potent inhibitors of human carbonic anhydrases II and VII and show neuropathic pain attenuating effects. Authors: Angeli, A. / Di Cesare Mannelli, L. / Ghelardini, C. / Peat, T.S. / Bartolucci, G. / Menicatti, M. / 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 | 6oe1.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oe1.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 6oe1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oe1_validation.pdf.gz | 703.2 KB | Display | wwPDB validaton report |
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Full document | 6oe1_full_validation.pdf.gz | 707.9 KB | Display | |
Data in XML | 6oe1_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6oe1_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/6oe1 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/6oe1 | HTTPS FTP |
-Related structure data
Related structure data | 6odzC 6oe0C 6c7xS S: Starting model for refinement C: citing same article (ref.) |
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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: 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, 320 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-M8V / |
#5: Chemical | ChemComp-SO4 / |
#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: 2.09 Å3/Da / Density % sol: 41.2 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 200 nL 7 mg/mL protein + 200 nL reservoir (50 mM Tris, pH 8.0-8.2, 2.5-2.8 M ammonium sulfate) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Apr 13, 2018 |
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: 1.45→40 Å / Num. obs: 39477 / % possible obs: 91.6 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.022 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 8.3 / Num. unique obs: 1476 / CC1/2: 0.983 / Rpim(I) all: 0.063 / % possible all: 69.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6C7X Resolution: 1.45→39.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.895 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.066 / 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: 9.234 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→39.98 Å
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Refine LS restraints |
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