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Yorodumi- PDB-4cq0: Cyclic secondary sulfonamides: unusually good inhibitors of cance... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cq0 | ||||||
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Title | Cyclic secondary sulfonamides: unusually good inhibitors of cancer- related carbonic anhydrase enzymes | ||||||
Components | CARBONIC ANHYDRASE 2 | ||||||
Keywords | LYASE / SACCHARIN / CLICK CHEMISTRY / DRUG DESIGN | ||||||
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 / 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: 1.45 Å | ||||||
Authors | Moeker, J. / Peat, T.S. / Bornaghi, L.F. / Vullo, D. / Supuran, C.T. / Poulsen, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Cyclic Secondary Sulfonamides: Unusually Good Inhibitors of Cancer-Related Carbonic Anhydrase Enzymes. Authors: Moeker, J. / Peat, T.S. / Bornaghi, L.F. / Vullo, D. / Supuran, C.T. / Poulsen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cq0.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cq0.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/4cq0 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/4cq0 | HTTPS FTP |
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-Related structure data
Related structure data | 3ml2S 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: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-FMT / |
#4: Chemical | ChemComp-SXS / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | LIGAND (SXS): SACCHARIN MOIETY |
-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: 41.7 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: THE PROTEIN WAS AT 14 MG/ML. THE RESERVOIR WAS 2.9 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5. THE DROPS WERE 210 NL PROTEIN PLUS 110 NL RESERVOIR PLUS 40 NL COMPOUND. THE CRYSTALS GREW AT 20C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 13, 2011 |
Radiation | 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→70 Å / Num. obs: 42055 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.6 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ML2 Resolution: 1.45→40.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.051 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.893 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→40.85 Å
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Refine LS restraints |
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