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Yorodumi- PDB-5sy3: Structure-based design of a new series of N-piperidin-3-ylpyrimid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5sy3 | |||||||||
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Title | Structure-based design of a new series of N-piperidin-3-ylpyrimidine-5-carboxamides as renin inhibitors | |||||||||
Components | Renin | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / protein-ligand complex / 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 / amyloid-beta metabolic process ...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 / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / 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 / molecular replacement / Resolution: 2.3 Å | |||||||||
Authors | Snell, G.P. / Behnke, C.A. / Okada, K. / Hideyuki, O. / Sang, B.C. / Lane, W. | |||||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2016 Title: Structure-based design of a new series of N-(piperidin-3-yl)pyrimidine-5-carboxamides as renin inhibitors. Authors: Imaeda, Y. / Tawada, M. / Suzuki, S. / Tomimoto, M. / Kondo, M. / Tarui, N. / Sanada, T. / Kanagawa, R. / Snell, G. / Behnke, C.A. / Kubo, K. / Kuroita, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sy3.cif.gz | 274 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sy3.ent.gz | 224.1 KB | Display | PDB format |
PDBx/mmJSON format | 5sy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/5sy3 ftp://data.pdbj.org/pub/pdb/validation_reports/sy/5sy3 | 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 37153.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P00797, renin |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 396 molecules
#4: Chemical | ChemComp-74Z / | ||||||
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#5: Chemical | ChemComp-DMS / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.33 % / Mosaicity: 0.819 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 23% PEG600, 0.06M citrate, 0.04M citric acid |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 21, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50.01 Å / Num. obs: 40166 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/av σ(I): 19.359 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.79 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.7 Å2 / Biso mean: 42.034 Å2 / Biso min: 18.01 Å2
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Refinement step | Cycle: final / Resolution: 2.3→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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