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Yorodumi- PDB-5tmk: Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Pep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tmk | ||||||
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Title | Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Peptide mimetics as an Orally Active Renin Inhibitor | ||||||
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 / 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 / molecular replacement / Resolution: 2.65 Å | ||||||
Authors | Snell, G.P. / Behnke, C.A. / Okada, K. / Hideyuki, O. / Sang, B.C. / Lane, W. | ||||||
Citation | Journal: To be published Title: Optimization of 3,5-Disubstitued Piperidine: Discovery of Non-Peptide mimetics as an Orally Active Renin Inhibitor Authors: Tokuhara, H. / Imaeda, Y. / Fukase, Y. / Iwanaga, K. / Taya, N. / Watanabe, K. / Kanagawa, R. / Matsuda, K. / Kajimoto, Y. / Kusumoto, K. / Kondo, M. / Snell, G.P. / Behnke, C.A. / Kuroita, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tmk.cif.gz | 261.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tmk.ent.gz | 216.2 KB | Display | PDB format |
PDBx/mmJSON format | 5tmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/5tmk ftp://data.pdbj.org/pub/pdb/validation_reports/tm/5tmk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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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, 3 molecules AB
#1: Protein | Mass: 36939.594 Da / Num. of mol.: 2 / Fragment: UNP residues 70-406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P00797, renin #2: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 47 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / | #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: 3.08 Å3/Da / Density % sol: 60.02 % / Mosaicity: 0.593 ° |
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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 315r / Detector: CCD / Date: Jan 18, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.65→50.01 Å / Num. obs: 26687 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Net I/av σ(I): 23.067 / Net I/σ(I): 14.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.65→50.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 21.919 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.551 / ESU R Free: 0.286 / Details: 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.45 Å2 / Biso mean: 74.423 Å2 / Biso min: 48.22 Å2
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Refinement step | Cycle: final / Resolution: 2.65→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.719 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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