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Yorodumi- PDB-4n4t: Co-crystal structure of tankyrase 1 with compound 3 [(4S)-3-{4-[6... -
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-Basic information
Entry | Database: PDB / ID: 4n4t | ||||||
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Title | Co-crystal structure of tankyrase 1 with compound 3 [(4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one] | ||||||
Components | Tankyrase-1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / tankyrase / PARP / Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information TCF dependent signaling in response to WNT / Degradation of AXIN / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / Regulation of PTEN stability and activity / cellular response to nutrient / Ub-specific processing proteases / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation ...TCF dependent signaling in response to WNT / Degradation of AXIN / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / Regulation of PTEN stability and activity / cellular response to nutrient / Ub-specific processing proteases / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / mRNA transport / nuclear pore / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / Wnt signaling pathway / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / protein transport / histone binding / nuclear membrane / chromosome, telomeric region / nuclear body / cell cycle / cell division / Golgi membrane / centrosome / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.315 Å | ||||||
Authors | Huang, X. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2013 Title: Structure-based design of 2-aminopyridine oxazolidinones as potent and selective tankyrase inhibitors. Authors: Huang, H. / Guzman-Perez, A. / Acquaviva, L. / Berry, V. / Bregman, H. / Dovey, J. / Gunaydin, H. / Huang, X. / Huang, L. / Saffran, D. / Serafino, R. / Schneider, S. / Wilson, C. / DiMauro, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n4t.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n4t.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/4n4t ftp://data.pdbj.org/pub/pdb/validation_reports/n4/4n4t | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 25041.332 Da / Num. of mol.: 2 / Fragment: UNP residues 1104-1314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnks, Tnks1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PFX9, NAD+ ADP-ribosyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2-0.4 M DiAmmonium Tartrate, 12.5-25% PEG 3350, pH 5.0-6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 21761 / % possible obs: 99.8 % / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.315→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.315→50 Å
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