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Yorodumi- PDB-4ryg: RENIN IN COMPLEXED WITH N-({(3S,4S)-4-[(benzylsulfonyl)amino]pyrr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ryg | ||||||
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Title | RENIN IN COMPLEXED WITH N-({(3S,4S)-4-[(benzylsulfonyl)amino]pyrrolidin-3-yl}methyl)-4-methoxy-3-(3-methoxypropoxy)-N-(propan-2-yl)benzamide INHIBITOR | ||||||
Components | Renin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins ...renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / amyloid-beta metabolic process / cell maturation / response to cAMP / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / kidney development / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Ostermann, N. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2015 Title: trans-(3S,4S)-Disubstituted pyrrolidines as inhibitors of the human aspartyl protease renin. Part I: Prime site exploration using an amino linker. Authors: Lorthiois, E. / Cumin, F. / Ehrhardt, C. / Kosaka, T. / Sellner, H. / Ostermann, N. / Francotte, E. / Wagner, T. / Maibaum, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ryg.cif.gz | 142.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ryg.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ryg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/4ryg ftp://data.pdbj.org/pub/pdb/validation_reports/ry/4ryg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 37267.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00797, renin #2: Sugar | |
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-Non-polymers , 4 types, 154 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: 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: 3.18 Å3/Da / Density % sol: 61.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: HANGING DROP, VAPOR DIFFUSION, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 9.4 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 18% PEG4000, 50 MM NACITRATE PH 4.0, 600 ...Details: HANGING DROP, VAPOR DIFFUSION, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 9.4 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 18% PEG4000, 50 MM NACITRATE PH 4.0, 600 MM NACL; SOAKING: DROP PLUS 2.5 UL RESERVOIR SOLUTION PLUS 10 MM INHIBITOR 54 AND 10% DMSO FOR 20 MIN; CRYO: SOAKING SOLUTION PLUS 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97865 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97865 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→42.72 Å / Num. obs: 27515 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 71.52 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→42.72 Å / Cor.coef. Fo:Fc: 0.9432 / Cor.coef. Fo:Fc free: 0.9164 / SU R Cruickshank DPI: 0.475 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 57.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.309 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→42.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.75 Å / Total num. of bins used: 14
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