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- PDB-5b4k: Crystal structure of the catalytic domain of human PDE10A complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b4k | ||||||
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Title | Crystal structure of the catalytic domain of human PDE10A complexed with N-(4-((5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy)phenyl)-1H-benzimidazol-2-amine | ||||||
![]() | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cGMP effects / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity ...cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cGMP effects / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cAMP-mediated signaling / G alpha (s) signalling events / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oki, H. / Zama, Y. | ||||||
![]() | ![]() Title: Design and synthesis of potent and selective pyridazin-4(1H)-one-based PDE10A inhibitors interacting with Tyr683 in the PDE10A selectivity pocket Authors: Yoshikawa, M. / Hitaka, T. / Hasui, T. / Fushimi, M. / Kunitomo, J. / Kokubo, H. / Oki, H. / Nakashima, K. / Taniguchi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 270.6 KB | Display | ![]() |
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PDB format | ![]() | 217.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 866.7 KB | Display | ![]() |
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Full document | ![]() | 868.2 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b4lC ![]() 3wymS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38889.586 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 442-779 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM HEPES pH 7.6, 100 mM magnesium chloride hexahydrate, 24.182% PEG 3350 PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→80.83 Å / Num. obs: 13970 / % possible obs: 90.9 % / Redundancy: 6 % / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.9→2.97 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WYM Resolution: 2.9→80.83 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.903 / SU B: 35.48 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.505
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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 mean: 56.224 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→80.83 Å
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Refine LS restraints |
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