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Yorodumi- PDB-4xx3: Renin in complex with (S)-1-(3-(benzylcarbamoyl)benzyl)-4-isoprop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xx3 | ||||||
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Title | Renin in complex with (S)-1-(3-(benzylcarbamoyl)benzyl)-4-isopropyl-4-methyl-6-oxotetrahydropyrimidin-2(1H)-iminium | ||||||
Components | Renin | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Animals / Antihypertensive Agents / Blood Pressure / Drug Design / Enzyme Inhibitors / Models / Molecular / Protein Conformation / Rats / Renin / Structure-Activity Relationship / 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 / amyloid-beta metabolic process / angiotensin maturation ...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 / amyloid-beta metabolic process / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / hormone-mediated signaling pathway / kidney development / insulin-like growth factor receptor binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Orth, P. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2015 Title: Iminopyrimidinones: a novel pharmacophore for the development of orally active renin inhibitors. Authors: McKittrick, B.A. / Caldwell, J.P. / Bara, T. / Boykow, G. / Chintala, M. / Clader, J. / Czarniecki, M. / Courneya, B. / Duffy, R. / Fleming, L. / Giessert, R. / Greenlee, W.J. / Heap, C. / ...Authors: McKittrick, B.A. / Caldwell, J.P. / Bara, T. / Boykow, G. / Chintala, M. / Clader, J. / Czarniecki, M. / Courneya, B. / Duffy, R. / Fleming, L. / Giessert, R. / Greenlee, W.J. / Heap, C. / Hong, L. / Huang, Y. / Iserloh, U. / Josien, H. / Khan, T. / Korfmacher, W. / Liang, X. / Mazzola, R. / Mitra, S. / Moore, K. / Orth, P. / Rajagopalan, M. / Roy, S. / Sakwa, S. / Strickland, C. / Vaccaro, H. / Voigt, J. / Wang, H. / Wong, J. / Zhang, R. / Zych, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xx3.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xx3.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xx3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4xx3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4xx3_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 4xx3_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/4xx3 ftp://data.pdbj.org/pub/pdb/validation_reports/xx/4xx3 | HTTPS FTP |
-Related structure data
Related structure data | 4s1gC 4xx4C 2i4qS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 37267.008 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): 293 HEK / Production host: Homo sapiens (human) / References: UniProt: P00797, renin #2: Sugar | #3: Chemical | #4: 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: 3.22 Å3/Da / Density % sol: 61.86 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Reservoir 15% PEG3350, 625 mM NaCl and citrate buffer pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 27, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 36678 / % possible obs: 97.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Χ2: 1.069 / Net I/av σ(I): 8.982 / Net I/σ(I): 11.1 / Num. measured all: 123848 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2I4Q Resolution: 2.4→47.34 Å / Cor.coef. Fo:Fc: 0.9403 / Cor.coef. Fo:Fc free: 0.9359 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 128.7 Å2 / Biso mean: 45.9629 Å2 / Biso min: 20.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.47 Å / Total num. of bins used: 18
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