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Yorodumi- PDB-8v42: Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8v42 | ||||||
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Title | Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400 | ||||||
Components | Serine/threonine-protein kinase VRK1 | ||||||
Keywords | TRANSFERASE / protein kinase / inhibitor / co-crystal | ||||||
Function / homology | Function and homology information histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation ...histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / Cajal body / nucleosomal DNA binding / neuron projection development / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / nucleolus / protein kinase binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Counago, R.M. / de Souza, G.P. / Azevedo, A. / Guimaraes, C. / Mascarello, A. / Gama, F. / Ferreira, M. / Arruda, P. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1 delta / epsilon. Authors: de Souza Gama, F.H. / Dutra, L.A. / Hawgood, M. / Dos Reis, C.V. / Serafim, R.A.M. / Ferreira Jr., M.A. / Teodoro, B.V.M. / Takarada, J.E. / Santiago, A.S. / Balourdas, D.I. / Nilsson, A.S. ...Authors: de Souza Gama, F.H. / Dutra, L.A. / Hawgood, M. / Dos Reis, C.V. / Serafim, R.A.M. / Ferreira Jr., M.A. / Teodoro, B.V.M. / Takarada, J.E. / Santiago, A.S. / Balourdas, D.I. / Nilsson, A.S. / Urien, B. / Almeida, V.M. / Gileadi, C. / Ramos, P.Z. / Salmazo, A. / Vasconcelos, S.N.S. / Cunha, M.R. / Mueller, S. / Knapp, S. / Massirer, K.B. / Elkins, J.M. / Gileadi, O. / Mascarello, A. / Lemmens, B.B.L.G. / Guimaraes, C.R.W. / Azevedo, H. / Counago, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v42.cif.gz | 487.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v42.ent.gz | 403.4 KB | Display | PDB format |
PDBx/mmJSON format | 8v42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v42_validation.pdf.gz | 991.4 KB | Display | wwPDB validaton report |
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Full document | 8v42_full_validation.pdf.gz | 996.7 KB | Display | |
Data in XML | 8v42_validation.xml.gz | 49 KB | Display | |
Data in CIF | 8v42_validation.cif.gz | 63.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/8v42 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/8v42 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 41138.125 Da / Num. of mol.: 4 Mutation: K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: Escherichia coli (E. coli) References: UniProt: Q99986, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-PEG / | #3: Chemical | Mass: 426.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16F2N6O3 #4: Chemical | ChemComp-SO4 / #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: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 22% PEG3350, 20 mM Li2SO4, 0.1 M Buffer system SBG pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.93 Å / Num. obs: 75682 / % possible obs: 99.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 13.8 % / Rmerge(I) obs: 2.417 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.93 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 14.927 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.201 Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.93 Å
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