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Yorodumi- PDB-6f23: Complex between MTH1 and compound 16 (a 4-amino-7-azaindole deriv... -
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-Basic information
Entry | Database: PDB / ID: 6f23 | ||||||
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Title | Complex between MTH1 and compound 16 (a 4-amino-7-azaindole derivative) | ||||||
Components | 7,8-dihydro-8-oxoguanine triphosphatase | ||||||
Keywords | HYDROLASE / NUDIX / NUCLEOTIDE HYDROLASE / INHIBITOR / ONCOLOGY | ||||||
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: 1.84 Å | ||||||
Authors | Viklund, J. / Tresaugues, L. / Talagas, A. / Andersson, M. / Ericsson, U. / Forsblom, R. / Ginman, T. / Hallberg, K. / Lindstrom, J. / Persson, L. ...Viklund, J. / Tresaugues, L. / Talagas, A. / Andersson, M. / Ericsson, U. / Forsblom, R. / Ginman, T. / Hallberg, K. / Lindstrom, J. / Persson, L. / Silvander, C. / Rahm, F. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Creation of a Novel Class of Potent and Selective MutT Homologue 1 (MTH1) Inhibitors Using Fragment-Based Screening and Structure-Based Drug Design. Authors: Rahm, F. / Viklund, J. / Tresaugues, L. / Ellermann, M. / Giese, A. / Ericsson, U. / Forsblom, R. / Ginman, T. / Gunther, J. / Hallberg, K. / Lindstrom, J. / Persson, L.B. / Silvander, C. / ...Authors: Rahm, F. / Viklund, J. / Tresaugues, L. / Ellermann, M. / Giese, A. / Ericsson, U. / Forsblom, R. / Ginman, T. / Gunther, J. / Hallberg, K. / Lindstrom, J. / Persson, L.B. / Silvander, C. / Talagas, A. / Diaz-Saez, L. / Fedorov, O. / Huber, K.V.M. / Panagakou, I. / Siejka, P. / Gorjanacz, M. / Bauser, M. / Andersson, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f23.cif.gz | 149 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f23.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 6f23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f23_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6f23_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6f23_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 6f23_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/6f23 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/6f23 | HTTPS FTP |
-Related structure data
Related structure data | 6f1xC 6f20C 6f22C 3q93S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18253.736 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Variant: Isoform p18 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.28 Å3/Da / Density % sol: 46.2 % / Description: Flat rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: 23% PEG 6000, 0.28M lithium sulfate, 0.1M sodium acetate pH 3.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972957 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 14, 2014 / Details: Toroidal mirror |
Radiation | Monochromator: Silicon (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972957 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→48.4 Å / Num. obs: 29541 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.063 / Net I/av σ(I): 7.9 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.84→1.9 Å / Redundancy: 6 % / Rmerge(I) obs: 1.877 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2846 / CC1/2: 0.518 / Rpim(I) all: 0.832 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q93 Resolution: 1.84→48.4 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.801 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.155 / 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: 30.885 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→48.4 Å
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Refine LS restraints |
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