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- PDB-8vxd: Structure of Casein kinase I isoform delta (CK1d) complexed with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vxd | ||||||
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Title | Structure of Casein kinase I isoform delta (CK1d) complexed with inhibitor 7 | ||||||
![]() | Casein kinase I isoform delta | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / CK1D / ![]() ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thompson, A.A. / Milligan, C.M. / Sharma, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure-Based Optimization of Selective and Brain Penetrant CK1 delta Inhibitors for the Treatment of Circadian Disruptions. Authors: McCarver, S. / Hanna, L. / Samant, A. / Thompson, A.A. / Seierstad, M. / Saha, A. / Wu, D. / Lord, B. / Sutton, S.W. / Shah, V. / Milligan, C.M. / Wennerholm, M. / Shelton, J. / Lebold, T.P. / Shireman, B.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 | ![]() | 241 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8vxeC ![]() 8vxfC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 34783.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P48730, ![]() ![]() #2: Chemical | Mass: 293.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12FN5 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 12%-20% PEG 10 K, 0.1 M Bis Tris (pH 5.5), 0.1 M Ammonium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.47→50.34 Å / Num. obs: 24239 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Net I/σ(I): 8.8 / Num. measured all: 80884 |
Reflection shell | Resolution: 2.47→2.51 Å / % possible obs: 92.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.678 / Num. measured all: 3844 / Num. unique obs: 1116 / CC1/2: 0.603 / Rpim(I) all: 0.428 / Rrim(I) all: 0.804 / Net I/σ(I) obs: 1.3 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→50.34 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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