+Open data
-Basic information
Entry | Database: PDB / ID: 6ym3 | ||||||
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Title | Crystal structure of Compound 1 with PIP4K2A | ||||||
Components | Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha | ||||||
Keywords | TRANSFERASE / PIP4K2A | ||||||
Function / homology | Function and homology information vesicle-mediated cholesterol transport / 1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / megakaryocyte development / PI5P Regulates TP53 Acetylation ...vesicle-mediated cholesterol transport / 1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / megakaryocyte development / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / photoreceptor outer segment / autophagosome / negative regulation of insulin receptor signaling pathway / photoreceptor inner segment / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / lysosome / phosphorylation / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Holton, S.J. / Wortmann, L. / Braeuer, N. / Irlbacher, H. / Weiske, J. / Lechner, C. / Meier, R. / Puetter, V. / Christ, C. / ter Laak, T. ...Holton, S.J. / Wortmann, L. / Braeuer, N. / Irlbacher, H. / Weiske, J. / Lechner, C. / Meier, R. / Puetter, V. / Christ, C. / ter Laak, T. / Lienau, P. / Lesche, R. / Nicke, B. / Bauser, M. / Haegebarth, A. / von Nussbaum, F. / Mumberg, D. / Lemos, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery and Characterization of the Potent and Highly Selective 1,7-Naphthyridine-Based Inhibitors BAY-091 and BAY-297 of the Kinase PIP4K2A. Authors: Wortmann, L. / Brauer, N. / Holton, S.J. / Irlbacher, H. / Weiske, J. / Lechner, C. / Meier, R. / Karen, J. / Sioberg, C.B. / Putter, V. / Christ, C.D. / Ter Laak, A. / Lienau, P. / Lesche, ...Authors: Wortmann, L. / Brauer, N. / Holton, S.J. / Irlbacher, H. / Weiske, J. / Lechner, C. / Meier, R. / Karen, J. / Sioberg, C.B. / Putter, V. / Christ, C.D. / Ter Laak, A. / Lienau, P. / Lesche, R. / Nicke, B. / Cheung, S.H. / Bauser, M. / Haegebarth, A. / von Nussbaum, F. / Mumberg, D. / Lemos, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ym3.cif.gz | 278.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ym3.ent.gz | 222.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ym3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ym3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ym3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ym3_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 6ym3_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/6ym3 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/6ym3 | HTTPS FTP |
-Related structure data
Related structure data | 6ym4C 6ym5C 2ybxS 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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Unit cell |
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-Components
#1: Protein | Mass: 45312.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2A, PIP5K2, PIP5K2A / Production host: Escherichia coli (E. coli) References: UniProt: P48426, 1-phosphatidylinositol-5-phosphate 4-kinase #2: Chemical | #3: Chemical | #4: 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: 2.48 Å3/Da / Density % sol: 50.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG3350, magnesium formate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→45.99 Å / Num. obs: 59573 / % possible obs: 99.3 % / Redundancy: 3.68 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.512 / Num. unique obs: 9014 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YBX Resolution: 2.05→45.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.248 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.166 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 122.71 Å2 / Biso mean: 42.319 Å2 / Biso min: 18.85 Å2
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Refinement step | Cycle: final / Resolution: 2.05→45.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Rfactor Rfree error: 0
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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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