+Open data
-Basic information
Entry | Database: PDB / ID: 3oad | ||||||
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Title | Design and optimization of new piperidines as renin inhibitors | ||||||
Components | (Renin) x 2 | ||||||
Keywords | HYDROLASE / Protease / Blood | ||||||
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 / Resolution: 2.17 Å | ||||||
Authors | Prade, L. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Design and optimization of new piperidines as renin inhibitors. Authors: Corminboeuf, O. / Bezencon, O. / Grisostomi, C. / Remen, L. / Richard-Bildstein, S. / Bur, D. / Prade, L. / Hess, P. / Strickner, P. / Fischli, W. / Steiner, B. / Treiber, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oad.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oad.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 3oad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/3oad ftp://data.pdbj.org/pub/pdb/validation_reports/oa/3oad | 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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Unit cell |
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-Components
#1: Protein | Mass: 18225.455 Da / Num. of mol.: 2 / Fragment: UNP RESIDUE 67-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00797, renin #2: Protein | Mass: 19430.055 Da / Num. of mol.: 2 / Fragment: UNP RESIDUE 237-406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00797, renin #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT A SEQUENCE COMPOSED OF FOUR RESIDUES (-233ENS236Q-) HAS BEEN CLEAVED AWAY TO ...AUTHORS STATE THAT A SEQUENCE COMPOSED OF FOUR RESIDUES (-233ENS236Q-) HAS BEEN CLEAVED AWAY TO ACTIVATE THE PROTEASE | |
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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: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.75 Details: 20-30% PEG 4000 0.6M KCl or NaCl, pH 4.75, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2006 |
Radiation | Monochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→59.1 Å / Num. all: 39861 / Num. obs: 35174 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.17→2.3 Å / % possible all: 37.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→59.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.451 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.256 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→59.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.225 Å / Total num. of bins used: 20
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