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- PDB-7k6j: Carbonic Anhydrase II complexed with 4-(2-(3-(4-methylphenyl)urei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k6j | ||||||
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Title | Carbonic Anhydrase II complexed with 4-(2-(3-(4-methylphenyl)ureido)ethylsulfonamido)benzenesulfonamide | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE/LYASE INHIBITOR / Carbonic Anhydrase CAII CAIX inhibitor Structure guided drug design Structure activity relationship study Breast Cancer / LYASE / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Andring, J.T. / Singh, S. / McKenna, R. | ||||||
![]() | ![]() Title: Handling drug-target selectivity: A study on ureido containing Carbonic Anhydrase inhibitors. Authors: Akgul, O. / Singh, S. / Andring, J.T. / McKenna, R. / Selleri, S. / Carta, F. / Angeli, A. / Supuran, C.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.5 KB | Display | ![]() |
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PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7k6iC ![]() 7k6kC ![]() 7k6lC ![]() 7k6tC ![]() 7k6uC ![]() 7k6xC ![]() 7k6zC ![]() 3ks3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 115 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/VYY.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/VYY.gif)
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#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-VYY / |
#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.61 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 1.6M Sodium Citrate, 50mM Tris, pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9177 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→32.06 Å / Num. obs: 24031 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 11.9 / Num. measured all: 160045 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ks3 Resolution: 1.755→30.492 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.02 / Stereochemistry target values: ML
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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 max: 67.25 Å2 / Biso mean: 19.163 Å2 / Biso min: 5.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.755→30.492 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -5.8817 Å / Origin y: -0.527 Å / Origin z: 85.2861 Å
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Refinement TLS group |
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