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Yorodumi- PDB-8vxf: Structure of Casein kinase I isoform delta (CK1d) complexed with ... -
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-Basic information
Entry | Database: PDB / ID: 8vxf | ||||||
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Title | Structure of Casein kinase I isoform delta (CK1d) complexed with inhibitor 15 | ||||||
Components | (Casein kinase I isoform delta) x 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / CK1D / KINASE / TRANSFERASE / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / midbrain dopaminergic neuron differentiation / COPII vesicle coating / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / ciliary basal body / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Thompson, A.A. / Milligan, C.M. / Sharma, S. | ||||||
Funding support | 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vxf.cif.gz | 244.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vxf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vxf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8vxf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8vxf_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 8vxf_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/8vxf ftp://data.pdbj.org/pub/pdb/validation_reports/vx/8vxf | HTTPS FTP |
-Related structure data
Related structure data | 8vxdC 8vxeC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 34799.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase | ||||
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#2: Protein | Mass: 34783.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase | ||||
#3: Chemical | Mass: 364.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17FN6O / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / 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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→54.38 Å / Num. obs: 29731 / % possible obs: 99.4 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.062 / Rrim(I) all: 0.113 / Net I/σ(I): 5.8 / Num. measured all: 97642 |
Reflection shell | Resolution: 2.28→2.32 Å / % possible obs: 89.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 1.097 / Num. measured all: 4491 / Num. unique obs: 1331 / CC1/2: 0.523 / Rpim(I) all: 0.701 / Rrim(I) all: 1.305 / Net I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→44.18 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.74 / Stereochemistry target values: ML
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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: 2.28→44.18 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.6926 Å / Origin y: 23.4491 Å / Origin z: -43.2713 Å
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Refinement TLS group | Selection details: all |