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Yorodumi- PDB-6kdx: Crystal structure of PDE10A in complex with a triazolopyrimidine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kdx | ||||||
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Title | Crystal structure of PDE10A in complex with a triazolopyrimidine inhibitor | ||||||
Components | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||
Keywords | HYDROLASE / Inhibitor | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Amano, Y. / Honbou, K. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2019 Title: Synthesis, SAR study, and biological evaluation of novel 2,3-dihydro-1H-imidazo[1,2-a]benzimidazole derivatives as phosphodiesterase 10A inhibitors. Authors: Chino, A. / Honda, S. / Morita, M. / Yonezawa, K. / Hamaguchi, W. / Amano, Y. / Moriguchi, H. / Yamazaki, M. / Aota, M. / Tomishima, M. / Masuda, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kdx.cif.gz | 146.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kdx.ent.gz | 113 KB | Display | PDB format |
PDBx/mmJSON format | 6kdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kdx_validation.pdf.gz | 698.8 KB | Display | wwPDB validaton report |
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Full document | 6kdx_full_validation.pdf.gz | 716.7 KB | Display | |
Data in XML | 6kdx_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 6kdx_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kdx ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kdx | HTTPS FTP |
-Related structure data
Related structure data | 6kdzC 6ke0C 2oupS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39606.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE10A / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-D6X / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.19 Å3/Da / Density % sol: 43.73 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 50mM Bis-tris propane pH6.0, 50mM Magnesium sulfate, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→50 Å / Num. obs: 23193 / % possible obs: 91.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.073 / Χ2: 2.357 / Net I/σ(I): 15.2 / Num. measured all: 125343 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OUP Resolution: 2.44→26.66 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / SU B: 13.261 / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.673 / ESU R Free: 0.379 / Details: 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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.75 Å2 / Biso mean: 56.869 Å2 / Biso min: 27.06 Å2
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Refinement step | Cycle: final / Resolution: 2.44→26.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.501 Å / Rfactor Rfree error: 0
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