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Open data
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Basic information
Entry | Database: PDB / ID: 6ahs | ||||||
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Title | Mouse Kallikrein 7 in complex with imidazolinylindole derivative | ||||||
![]() | Kallikrein-7 | ||||||
![]() | HYDROLASE / protease | ||||||
Function / homology | ![]() stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / Degradation of the extracellular matrix / cornified envelope / secretory granule / serine-type endopeptidase activity / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sugawara, H. | ||||||
![]() | ![]() Title: Discovery and structure-activity relationship of imidazolinylindole derivatives as kallikrein 7 inhibitors. Authors: Murafuji, H. / Muto, T. / Goto, M. / Imajo, S. / Sugawara, H. / Oyama, Y. / Minamitsuji, Y. / Miyazaki, S. / Murai, K. / Fujioka, H. #1: ![]() Title: Discovery and structure-activity relationship study of 1,3,6-trisubstituted 1,4-diazepane-7-ones as novel human kallikrein 7 inhibitors. Authors: Murafuji, H. / Sakai, H. / Goto, M. / Imajo, S. / Sugawara, H. / Muto, T. #2: Journal: Bioorg. Med. Chem. Lett. / Year: 2018 Title: Structure-based drug design of 1,3,6-trisubstituted 1,4-diazepan-7-ones as selective human kallikrein 7 inhibitors. Authors: Murafuji, H. / Sakai, H. / Goto, M. / Oyama, Y. / Imajo, S. / Sugawara, H. / Tomoo, T. / Muto, T. #3: ![]() Title: Structure-based drug design to overcome species differences in kallikrein 7 inhibition of 1,3,6-trisubstituted 1,4-diazepan-7-ones. Authors: Murafuji, H. / Sugawara, H. / Goto, M. / Oyama, Y. / Sakai, H. / Imajo, S. / Tomoo, T. / Muto, 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 | ![]() | 104.7 KB | Display | ![]() |
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PDB format | ![]() | 78.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 856.2 KB | Display | ![]() |
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Full document | ![]() | 856.1 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zfhS S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 24637.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q91VE3, stratum corneum chymotryptic enzyme | ||
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#2: Chemical | ChemComp-9YO / | ||
#3: Chemical | ChemComp-TRS / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 8000, PEG 400, magnesium chloride, Tris/HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→100 Å / Num. obs: 26249 / % possible obs: 99.1 % / Redundancy: 13.2 % / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.75→1.78 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZFH Resolution: 1.75→30.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.055 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / 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: 29.665 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→30.29 Å
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Refine LS restraints |
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