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Yorodumi- PDB-5ngt: Crystal structure of human MTH1 in complex with inhibitor 7-(fura... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ngt | |||||||||||||||||||||||||||||||||||||||
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Title | Crystal structure of human MTH1 in complex with inhibitor 7-(furan-2-yl)-5-methyl-1,3-benzoxazol-2-amine | |||||||||||||||||||||||||||||||||||||||
Components | 7,8-dihydro-8-oxoguanine triphosphatase | |||||||||||||||||||||||||||||||||||||||
Keywords | HYDROLASE / Inhibitor / Fragment / Oxidised nucleotides | |||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information 2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity ...2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to cadmium ion / acrosomal vesicle / male gonad development / nuclear membrane / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / extracellular space / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Gustafsson, R. / Rudling, A. / Almlof, I. / Homan, E. / Scobie, M. / Warpman Berglund, U. / Helleday, T. / Carlsson, J. / Stenmark, P. | |||||||||||||||||||||||||||||||||||||||
Funding support | Sweden, 12items
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Citation | Journal: J. Med. Chem. / Year: 2017 Title: Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space. Authors: Rudling, A. / Gustafsson, R. / Almlof, I. / Homan, E. / Scobie, M. / Warpman Berglund, U. / Helleday, T. / Stenmark, P. / Carlsson, J. | |||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ngt.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ngt.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ngt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/5ngt ftp://data.pdbj.org/pub/pdb/validation_reports/ng/5ngt | HTTPS FTP |
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-Related structure data
Related structure data | 5ngrC 5ngsC 3zr1S C: citing same article (ref.) S: Starting model for refinement |
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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: 18253.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase | ||
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#2: Chemical | ChemComp-8WZ / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 5 mmol/L compound and 6 mmol/L MgCl2 were added to MTH1. Sitting drop vapor diffusion experiments at 293K were performed, and MTH1 (9.34 mg/mL) was mixed with reservoir solution (32% (w/v) ...Details: 5 mmol/L compound and 6 mmol/L MgCl2 were added to MTH1. Sitting drop vapor diffusion experiments at 293K were performed, and MTH1 (9.34 mg/mL) was mixed with reservoir solution (32% (w/v) PEG3350, 0.1 mol/L Sodium Acetate pH 4.0 and 0.2 mol/L LiSO4) in a 1:1 ratio. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→44.85 Å / Num. obs: 22455 / % possible obs: 0.994 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.54→1.56 Å / Redundancy: 7 % / Rmerge(I) obs: 1.182 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1056 / CC1/2: 0.559 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZR1 Resolution: 1.54→44.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.759 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.577 Å2
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Refinement step | Cycle: 1 / Resolution: 1.54→44.85 Å
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