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- PDB-5anw: MTH1 in complex with compound 24 -

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Basic information

Entry
Database: PDB / ID: 5anw
TitleMTH1 in complex with compound 24
Components7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
KeywordsHYDROLASE / NUDT1 / NUDIX HYDROLASE / INHIBITOR
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
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Oxidized purine nucleoside triphosphate / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-9CQ / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsRead, J.A. / Breed, J.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Potent and Selective Inhibitors of Mth1 Probe its Role in Cancer Cell Survival.
Authors: Kettle, J.G. / Alwan, H. / Bista, M. / Breed, J. / Davies, N.L. / Eckersley, K. / Fillery, S. / Foote, K.M. / Goodwin, L. / Jones, D.R. / Kack, H. / Lau, A. / Nissink, J.W. / Read, J. / ...Authors: Kettle, J.G. / Alwan, H. / Bista, M. / Breed, J. / Davies, N.L. / Eckersley, K. / Fillery, S. / Foote, K.M. / Goodwin, L. / Jones, D.R. / Kack, H. / Lau, A. / Nissink, J.W. / Read, J. / Scott, J.S. / Taylor, B. / Walker, G. / Wissler, L. / Wylot, M.
History
DepositionSep 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Atomic model
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4062
Polymers18,1001
Non-polymers3061
Water1,31573
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.130, 66.070, 35.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2029-

HOH

21A-2068-

HOH

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Components

#1: Protein 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE / MTH1 / 2-HYDROXY-DATP DIPHOSPHATASE / 8-OXO-DGTPASE / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF ...MTH1 / 2-HYDROXY-DATP DIPHOSPHATASE / 8-OXO-DGTPASE / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1 / NUDIX MOTIF 1


Mass: 18099.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: P36639, 8-oxo-dGTP diphosphatase, 2-hydroxy-dATP diphosphatase
#2: Chemical ChemComp-9CQ / 2-[4-(2-AMINOQUINAZOLIN-4-YL)PHENYL]-N,N-DIMETHYL-ACETAMIDE


Mass: 306.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.72 % / Description: NONE
Crystal growpH: 4.5 / Details: pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 4, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.37→61.1 Å / Num. obs: 25048 / % possible obs: 80 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 13.27 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.6
Reflection shellResolution: 1.37→1.41 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.8 / % possible all: 17

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→15.86 Å / Cor.coef. Fo:Fc: 0.9419 / Cor.coef. Fo:Fc free: 0.9352 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.078 / SU Rfree Cruickshank DPI: 0.077
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 1218 4.88 %RANDOM
Rwork0.1989 ---
obs0.2003 24983 79.71 %-
Displacement parametersBiso mean: 14.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.2861 Å20 Å20 Å2
2--0.5173 Å20 Å2
3----0.8033 Å2
Refine analyzeLuzzati coordinate error obs: 0.198 Å
Refinement stepCycle: LAST / Resolution: 1.37→15.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 23 73 1306
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081320HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.971804HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d438SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes198HARMONIC5
X-RAY DIFFRACTIONt_it1320HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.09
X-RAY DIFFRACTIONt_other_torsion14.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion160SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1494SEMIHARMONIC4
LS refinement shellResolution: 1.37→1.43 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3417 32 4.23 %
Rwork0.3707 724 -
all0.3693 756 -
obs--21.77 %
Refinement TLS params.Method: refined / Origin x: 14.2828 Å / Origin y: 19.754 Å / Origin z: 9.2814 Å
111213212223313233
T-0.0126 Å20.0081 Å2-0.0089 Å2-0.0017 Å20.0027 Å2---0.0076 Å2
L0.8015 °20.464 °2-0.0704 °2-1.2662 °2-0.1466 °2--0.6698 °2
S0.041 Å °0.0228 Å °-0.037 Å °0.0549 Å °0.003 Å °0.0204 Å °0.003 Å °-0.0375 Å °-0.044 Å °
Refinement TLS groupSelection details: { A|3 - A|156 }

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