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- PDB-7k6u: Carbonic Anhydrase IX mimic complexed with 4-(2-(3-(4-methylpheny... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k6u | ||||||
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Title | Carbonic Anhydrase IX mimic 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 / cytoplasm / cytosol 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 | ![]() | 122.2 KB | Display | ![]() |
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PDB format | ![]() | 91.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773.9 KB | Display | ![]() |
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Full document | ![]() | 776.7 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k6iC ![]() 7k6jC ![]() 7k6kC ![]() 7k6lC ![]() 7k6tC ![]() 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
#1: Protein | Mass: 29200.887 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-VYY / |
#4: Chemical | ChemComp-DMS / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % |
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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: 1.605→32.05 Å / Num. obs: 31486 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Net I/σ(I): 13 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.2 %
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ks3 Resolution: 1.605→23.318 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.53 / 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: 82.23 Å2 / Biso mean: 20.0873 Å2 / Biso min: 6.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.605→23.318 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: -5.3797 Å / Origin y: -1.7449 Å / Origin z: 86.0329 Å
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Refinement TLS group |
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