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Yorodumi- PDB-4c1i: Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Acti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c1i | ||||||
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Title | Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System | ||||||
Components | CGMP-DEPENDENT 3', 5'-CYCLIC PHOSPHODIESTERASE | ||||||
Keywords | HYDROLASE / HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information regulation of cGMP-mediated signaling / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of vascular permeability / heart valve development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier ...regulation of cGMP-mediated signaling / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of vascular permeability / heart valve development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / regulation of mitochondrion organization / aorta development / ventricular septum development / cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / TPR domain binding / cGMP-mediated signaling / cGMP catabolic process / phosphate ion binding / cGMP effects / monocyte differentiation / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of cAMP-mediated signaling / cAMP binding / cellular response to cAMP / cellular response to transforming growth factor beta stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cAMP-mediated signaling / synaptic membrane / positive regulation of inflammatory response / cellular response to mechanical stimulus / cellular response to xenobiotic stimulus / presynaptic membrane / G alpha (s) signalling events / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Jorgensen, M. / Kehler, J. / Langgard, M. / Svenstrup, N. / Tagmose, L. | ||||||
Citation | Journal: To be Published Title: Chapter 4: Selective Inhibitors of Pde2, Pde9, and Pde10: Modulators of Activity of the Central Nervous System Authors: Jorgensen, M. / Kehler, J. / Langgard, M. / Svenstrup, N. / Tagmose, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c1i.cif.gz | 270.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c1i.ent.gz | 217.8 KB | Display | PDB format |
PDBx/mmJSON format | 4c1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c1i_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4c1i_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4c1i_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 4c1i_validation.cif.gz | 64.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/4c1i ftp://data.pdbj.org/pub/pdb/validation_reports/c1/4c1i | HTTPS FTP |
-Related structure data
Related structure data | 1z1lS S: Starting model for refinement |
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Similar 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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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 41432.375 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 578-921 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: O00408, 3',5'-cyclic-nucleotide phosphodiesterase #2: Chemical | ChemComp-EH9 / ( #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: 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: 2 Å3/Da / Density % sol: 39 % / Description: NONE |
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Crystal grow | pH: 8.6 Details: 14% PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.1 M TRIS HYDROCHLORIDE PH 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Jun 12, 2008 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→18.47 Å / Num. obs: 47638 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2 / % possible all: 91.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z1L Resolution: 2.4→18.47 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.872 / SU B: 11.146 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 1.166 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 mean: 29.988 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→18.47 Å
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