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Yorodumi- PDB-3n4c: 6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n4c | ||||||
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Title | 6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S inhibitors | ||||||
Components | Cathepsin S | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Cathepsin S / covalent inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / antigen processing and presentation / collagen catabolic process / extracellular matrix disassembly / laminin binding / phagocytic vesicle / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / Endosomal/Vacuolar pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / adaptive immune response / ficolin-1-rich granule lumen / lysosome / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Fradera, X. / Uitdehaag, J.C.M. / van Zeeland, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: 6-Phenyl-1H-imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S inhibitors. Authors: Cai, J. / Baugh, M. / Black, D. / Long, C. / Jonathan Bennett, D. / Dempster, M. / Fradera, X. / Gillespie, J. / Andrews, F. / Boucharens, S. / Bruin, J. / Cameron, K.S. / Cumming, I. / ...Authors: Cai, J. / Baugh, M. / Black, D. / Long, C. / Jonathan Bennett, D. / Dempster, M. / Fradera, X. / Gillespie, J. / Andrews, F. / Boucharens, S. / Bruin, J. / Cameron, K.S. / Cumming, I. / Hamilton, W. / Jones, P.S. / Kaptein, A. / Kinghorn, E. / Maidment, M. / Martin, I. / Mitchell, A. / Rankovic, Z. / Robinson, J. / Scullion, P. / Uitdehaag, J.C. / Vink, P. / Westwood, P. / van Zeeland, M. / van Berkom, L. / Bastiani, M. / Meulemans, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n4c.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n4c.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 3n4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n4c ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n4c | HTTPS FTP |
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-Related structure data
Related structure data | 1ms6S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24006.936 Da / Num. of mol.: 2 / Fragment: UNP residues 115 to 331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: sapiens / Gene: CTSS, Homo sapiens / Plasmid: baculovirus / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-Tn-5B1-4 (Hi-5) / References: UniProt: P25774, cathepsin S #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.21 % |
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Crystal grow | Method: hanging drop / pH: 5 Details: Composition of crystallisation solution (including components from protein prep): 50 mM NaAcetate; 0.25 M NaCl; coconcentrated with inhibitor; 4% DMSO; 26% PEG 4K; 0.1 M NaCitrate pH=5.0; ...Details: Composition of crystallisation solution (including components from protein prep): 50 mM NaAcetate; 0.25 M NaCl; coconcentrated with inhibitor; 4% DMSO; 26% PEG 4K; 0.1 M NaCitrate pH=5.0; 0,2 M (NH4)2SO4. Cryoprotectant composition: 26% PEG 4K, 0.1 M NaCitrate pH=5.0; o0.2 M (NH4)2SO4; 15% PEG 400 (compound), Hanging drop, temperature room temperatureK |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: R-Axis IV / Detector: CCD / Date: Dec 11, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→56.54 Å / Num. obs: 39256 / % possible obs: 87.4 % / Redundancy: 6.82 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MS6 Resolution: 1.9→56.54 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.519 / SU ML: 0.108 / SU R Cruickshank DPI: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.801 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→56.54 Å
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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