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- PDB-9xri: Crystal structure of MTH1 in complex with acoramidis bound at the... -

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Basic information

Entry
Database: PDB / ID: 9xri
TitleCrystal structure of MTH1 in complex with acoramidis bound at the active site and protein-protein interface (molar ratio 1:24)
ComponentsOxidized purine nucleoside triphosphate hydrolase
KeywordsHYDROLASE / inhibitor / cancer / NUDIX hydrolase / drug repositioning
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 / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...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 / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Chem-16V / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsYokoyama, T. / Nakamura, T. / Goto, M. / Kusaka, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K09746 Japan
CitationJournal: Acs Pharmacol Transl Sci / Year: 2026
Title: Identification of Acoramidis as a Repurposed Inhibitor of the DNA Sanitization Enzyme MutT Homologue 1.
Authors: Yokoyama, T. / Nakamura, T. / Goto, M. / Kusaka, K.
History
DepositionNov 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidized purine nucleoside triphosphate hydrolase
B: Oxidized purine nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8098
Polymers36,0552
Non-polymers1,7546
Water7,332407
1
A: Oxidized purine nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9044
Polymers18,0281
Non-polymers8773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidized purine nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9044
Polymers18,0281
Non-polymers8773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.950, 47.870, 124.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oxidized purine nucleoside triphosphate hydrolase / 2-hydroxy-dATP diphosphatase / 7 / 8-dihydro-8-oxoguanine triphosphatase / 8-oxo-dGTPase / ...2-hydroxy-dATP diphosphatase / 7 / 8-dihydro-8-oxoguanine triphosphatase / 8-oxo-dGTPase / Methylated purine nucleoside triphosphate hydrolase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18027.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P36639, 2-hydroxy-dATP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-16V / 3-[3-(3,5-dimethyl-1H-pyrazol-4-yl)propoxy]-4-fluorobenzoic acid


Mass: 292.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H17FN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1M sodium citrate, 0.2M sodium chloride, 0.1M cacodylate pH 6.5, 8mM acoramidis

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.08→37.92 Å / Num. obs: 118172 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rrim(I) all: 0.091 / Net I/σ(I): 9.9
Reflection shellResolution: 1.08→1.11 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8656 / CC1/2: 0.817 / Rrim(I) all: 0.687 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XSCALEdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→37.92 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1728 5909 5 %
Rwork0.1561 --
obs0.1569 118169 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.08→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 126 407 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052759
X-RAY DIFFRACTIONf_angle_d0.8983731
X-RAY DIFFRACTIONf_dihedral_angle_d19.6441045
X-RAY DIFFRACTIONf_chiral_restr0.076369
X-RAY DIFFRACTIONf_plane_restr0.007482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.22811970.1973736X-RAY DIFFRACTION100
1.09-1.110.2261930.18673683X-RAY DIFFRACTION100
1.11-1.120.18621950.17383692X-RAY DIFFRACTION100
1.12-1.130.1991920.1653648X-RAY DIFFRACTION100
1.13-1.150.20651970.1663741X-RAY DIFFRACTION100
1.15-1.160.20241950.16363704X-RAY DIFFRACTION100
1.16-1.180.18141950.15963709X-RAY DIFFRACTION100
1.18-1.20.16941940.15273684X-RAY DIFFRACTION100
1.2-1.220.18511960.15093719X-RAY DIFFRACTION100
1.22-1.240.21191960.1443726X-RAY DIFFRACTION100
1.24-1.260.1791940.14883689X-RAY DIFFRACTION100
1.26-1.280.18511960.14523728X-RAY DIFFRACTION100
1.28-1.310.17711950.14673698X-RAY DIFFRACTION100
1.31-1.330.1751960.14443723X-RAY DIFFRACTION100
1.33-1.360.16181950.14423711X-RAY DIFFRACTION100
1.36-1.390.17371950.14753716X-RAY DIFFRACTION100
1.39-1.430.18571960.14623707X-RAY DIFFRACTION100
1.43-1.470.16061960.13933731X-RAY DIFFRACTION100
1.47-1.510.15881970.13263752X-RAY DIFFRACTION100
1.51-1.560.17051960.13433717X-RAY DIFFRACTION100
1.56-1.610.17281970.13863746X-RAY DIFFRACTION100
1.61-1.680.16331970.14383741X-RAY DIFFRACTION100
1.68-1.750.16861980.15033758X-RAY DIFFRACTION100
1.75-1.850.20361990.15743778X-RAY DIFFRACTION100
1.85-1.960.14711960.15033737X-RAY DIFFRACTION100
1.96-2.110.15772000.1543791X-RAY DIFFRACTION100
2.11-2.330.16911990.1553780X-RAY DIFFRACTION100
2.33-2.660.1942020.17743842X-RAY DIFFRACTION100
2.66-3.350.18072020.17613836X-RAY DIFFRACTION100
3.36-37.920.14922130.15244037X-RAY DIFFRACTION100

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