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- PDB-5c2h: PDE10 complexed with 6-chloro-N-[(2,4-dimethylthiazol-5-yl)methyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5c2h | ||||||
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Title | PDE10 complexed with 6-chloro-N-[(2,4-dimethylthiazol-5-yl)methyl]-5-methyl-2-[3-(2-quinolyl)propoxy]pyrimidin-4-amine | ||||||
![]() | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||
![]() | hydrolase/hydrolase inhibitor / Phosphodiesterase / inhibitor / complex / 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 | ![]() ![]() ![]() | ||||||
![]() | Yan, Y. | ||||||
![]() | ![]() Title: Discovery and Optimization of a Series of Pyrimidine-Based Phosphodiesterase 10A (PDE10A) Inhibitors through Fragment Screening, Structure-Based Design, and Parallel Synthesis. Authors: Shipe, W.D. / Sharik, S.S. / Barrow, J.C. / McGaughey, G.B. / Theberge, C.R. / Uslaner, J.M. / Yan, Y. / Renger, J.J. / Smith, S.M. / Coleman, P.J. / Cox, C.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.6 KB | Display | ![]() |
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PDB format | ![]() | 110.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5c1wC ![]() 5c28C ![]() 5c29C ![]() 5c2aC ![]() 5c2eC ![]() 4zo5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41495.504 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase |
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-Non-polymers , 5 types, 68 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/4PX.gif)
![](data/chem/img/4XU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/4PX.gif)
![](data/chem/img/4XU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-4PX / | #5: Chemical | ChemComp-4XU / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES, 20% PEG3350, 200mM MgCl2, and 10mM 2-Mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→50 Å / Num. obs: 88979 / % possible obs: 98.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.47 Å2 / Rmerge(I) obs: 0.051 / Χ2: 0.968 / Net I/av σ(I): 28.013 / Net I/σ(I): 15.2 / Num. measured all: 548846 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZO5 Resolution: 2.09→36.1 Å / Cor.coef. Fo:Fc: 0.9204 / Cor.coef. Fo:Fc free: 0.8893 / SU R Cruickshank DPI: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.281 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.204
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Displacement parameters | Biso max: 123.89 Å2 / Biso mean: 47.13 Å2 / Biso min: 22.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.309 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→36.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.15 Å / Total num. of bins used: 17
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