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- PDB-6f1x: Complex between MTH1 and compound 7 (a 7-azaindole-2-amide derivative) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f1x | ||||||
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Title | Complex between MTH1 and compound 7 (a 7-azaindole-2-amide derivative) | ||||||
![]() | 7,8-dihydro-8-oxoguanine triphosphatase | ||||||
![]() | HYDROLASE / NUDIX / NUCLEOTIDE HYDROLASE / INHIBITOR / ONCOLOGY | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Viklund, J. / Talagas, A. / Tresaugues, L. / Andersson, M. / Ericsson, U. / Forsblom, R. / Ginman, T. / Hallberg, K. / Lindstrom, J. / Persson, L. ...Viklund, J. / Talagas, A. / Tresaugues, L. / Andersson, M. / Ericsson, U. / Forsblom, R. / Ginman, T. / Hallberg, K. / Lindstrom, J. / Persson, L. / Silvander, C. / Rahm, F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.9 KB | Display | ![]() |
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PDB format | ![]() | 61.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6f20C ![]() 6f22C ![]() 6f23C ![]() 3q93S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 18253.736 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FULL LENGTH HUMAN MTH1 ISOFORM P18 CONTAINING RESIDUALS FROM A THROMBIN-CLEAVAGE SITE IN N-TERMINUS Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.6 / Details: 26% PEG6000, 0.1M Na-acetate pH 3.6, 0.22M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.68 Å / Num. obs: 26731 / % possible obs: 98.8 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.047 / Rrim(I) all: 0.171 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.732 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2581 / CC1/2: 0.597 / Rpim(I) all: 0.498 / Rrim(I) all: 1.804 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q93 Resolution: 1.9→48.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.153 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / 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: 28.308 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→48.68 Å
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Refine LS restraints |
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