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- PDB-6t5j: Structure of NUDT15 in complex with inhibitor TH1760 -

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Basic information

Entry
Database: PDB / ID: 6t5j
TitleStructure of NUDT15 in complex with inhibitor TH1760
ComponentsProbable 8-oxo-dGTP diphosphatase NUDT15
KeywordsHYDROLASE / Nudix hydrolase / Inhibitor
Function / homology
Function and homology information


nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection ...nucleoside phosphate catabolic process / purine nucleotide catabolic process / nucleotide diphosphatase / nucleobase-containing small molecule metabolic process / nucleoside triphosphate diphosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA protection / Phosphate bond hydrolysis by NUDT proteins / Azathioprine ADME / regulation of proteasomal protein catabolic process / xenobiotic catabolic process / response to reactive oxygen species / mitotic cell cycle / metal ion binding / cytosol
Similarity search - Function
NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Chem-MKB / Nucleotide triphosphate diphosphatase NUDT15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCarter, M. / Rehling, D. / Desroses, M. / Zhang, S.M. / Hagenkort, A. / Valerie, N.C.K. / Helleday, T. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Development of a chemical probe against NUDT15.
Authors: Zhang, S.M. / Desroses, M. / Hagenkort, A. / Valerie, N.C.K. / Rehling, D. / Carter, M. / Wallner, O. / Koolmeister, T. / Throup, A. / Jemth, A.S. / Almlof, I. / Loseva, O. / Lundback, T. / ...Authors: Zhang, S.M. / Desroses, M. / Hagenkort, A. / Valerie, N.C.K. / Rehling, D. / Carter, M. / Wallner, O. / Koolmeister, T. / Throup, A. / Jemth, A.S. / Almlof, I. / Loseva, O. / Lundback, T. / Axelsson, H. / Regmi, S. / Sarno, A. / Kramer, A. / Pudelko, L. / Brautigam, L. / Rasti, A. / Gottmann, M. / Wiita, E. / Kutzner, J. / Schaller, T. / Kalderen, C. / Cazares-Korner, A. / Page, B.D.G. / Krimpenfort, R. / Eshtad, S. / Altun, M. / Rudd, S.G. / Knapp, S. / Scobie, M. / Homan, E.J. / Berglund, U.W. / Stenmark, P. / Helleday, T.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 8-oxo-dGTP diphosphatase NUDT15
B: Probable 8-oxo-dGTP diphosphatase NUDT15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,29110
Polymers37,2702
Non-polymers1,0218
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-56 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.790, 46.809, 137.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Probable 8-oxo-dGTP diphosphatase NUDT15 / 8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / ...8-oxo-dGTPase NUDT15 / 7 / 8-dihydro-8-oxoguanine-triphosphatase NUDT15 / MutT homolog 2 / MTH2 / Nucleoside diphosphate-linked moiety X motif 15 / Nudix motif 15


Mass: 18635.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT15, MTH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NV35, nucleotide diphosphatase
#2: Chemical ChemComp-MKB / 6-[4-(1~{H}-indol-5-ylcarbonyl)piperazin-1-yl]sulfonyl-3~{H}-1,3-benzoxazol-2-one


Mass: 426.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18N4O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.15 M MgCl2, and 30% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.6→46.81 Å / Num. obs: 40092 / % possible obs: 98.6 % / Redundancy: 11.9 % / Biso Wilson estimate: 13.15 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.056 / Rrim(I) all: 0.143 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
8.76-46.810.06822.73050.9980.0270.074
1.6-1.6312.40.554.219130.8430.2310.59797.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LPG

5lpg


Resolution: 1.6→44.31 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.9696
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 2096 5.23 %Random selection
Rwork0.1612 ---
obs0.1629 40061 98.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.89 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 66 454 3006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732660
X-RAY DIFFRACTIONf_angle_d0.78853623
X-RAY DIFFRACTIONf_chiral_restr0.0561355
X-RAY DIFFRACTIONf_plane_restr0.0046469
X-RAY DIFFRACTIONf_dihedral_angle_d13.5807965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.26681230.22822460X-RAY DIFFRACTION97.21
1.64-1.680.26441420.21442471X-RAY DIFFRACTION97.1
1.68-1.720.25271580.2112432X-RAY DIFFRACTION97.22
1.72-1.770.23231330.19582496X-RAY DIFFRACTION97.7
1.77-1.830.21311300.18312459X-RAY DIFFRACTION97.51
1.83-1.90.21031450.1742511X-RAY DIFFRACTION97.83
1.9-1.970.19981300.16232477X-RAY DIFFRACTION97.68
1.97-2.060.1941670.15152480X-RAY DIFFRACTION98.15
2.06-2.170.17841350.14832526X-RAY DIFFRACTION98.45
2.17-2.310.19971150.14492544X-RAY DIFFRACTION98.37
2.31-2.490.19261340.15332566X-RAY DIFFRACTION98.79
2.49-2.740.17951420.15342570X-RAY DIFFRACTION98.83
2.74-3.130.16811560.15652575X-RAY DIFFRACTION99.09
3.13-3.950.18131340.13892633X-RAY DIFFRACTION99.43
3.95-44.30.18561520.16152760X-RAY DIFFRACTION99.45
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.87618687755-1.94644930086-0.7256186869263.10766727482.736924523264.02957880876-0.203729918203-0.6540595010980.625778672870.215197967729-0.197862531276-0.0169853051368-0.6609436739460.1762685888880.3908794941280.206824991025-0.0754008516482-0.0441354101590.235118015349-0.03817604562380.215797401223-8.4919281830325.656997908-12.5211720688
23.120884904690.4219733423030.4338015816224.697701453861.23706058763.234011255970.07647611171330.0437792271588-0.275553865888-0.100378524291-0.096467464713-0.1276235273870.4318796803670.0614275879431-0.0002919082500090.104468699522-0.005044082162040.005139859770470.0838868067214-0.002198270040910.0648886086243-9.63617853417-1.26289467515-23.5499657728
36.173479704060.3680597632132.047920028471.905153562560.2669735480626.606645124720.3926730788-0.280476408457-0.4472282271410.167240337223-0.0130482242538-0.387460301784-0.1175480450870.402125463958-0.3201019323860.12031181066-0.0267807961745-0.02720755515040.151003349167-0.009263261663590.1633738225841.188646266666.35628034967-13.8120807257
45.27382008727-2.115936998240.9986704481288.18587180507-3.577396619614.899088240640.1930320612620.01537472687540.548715300482-0.0956598195667-0.265879648234-0.402841269777-0.330958646760.3182042144140.04454343776860.0851679699747-0.02832007782490.03978637902210.1179098772290.01761035162180.137913162635-7.8910692652420.621707131-25.6899235534
51.01544588774-0.961167998326-1.100592013691.920540168581.08416941672.415281632330.0704268018760.1263368245790.0193425282786-0.101099531601-0.102058721621-0.0274879257162-0.05263713130950.04767160591580.0213321587840.054176646295-0.000555163909981-0.00593844897530.08691968147020.002738037378220.060782331103-10.496192253210.5310085863-25.8547541137
63.341865481184.638548489160.9951408134056.512938695010.9006200646664.626722989670.000857165208536-0.568421580832-0.1350204805160.4944330273170.0528962384141-1.109352561620.3036935280950.587276409254-0.1155334333230.1680625398220.0463088936575-0.08002870846080.372680608894-0.04789906866410.294403654005-3.3811120926417.9876810354-4.65388054211
70.613408571497-0.59497754466-1.190471894693.441458485643.709818696216.69292906078-0.09492181809110.0532114132842-0.01888490103190.08568863106520.06397974506910.02928095700360.2927385552280.2830548933310.01886606459260.07394683150830.0135028800457-0.01921582017060.08657848742380.004137523170120.0683493141085-10.42040920526.71790891661-25.9233380378
82.762514377782.618604040363.851319708192.585881356643.667322701475.709907894890.00915309609010.111962629813-0.157299852928-0.122850633345-0.0358949814694-0.48600953307-0.04701143123090.4801353078460.04204007145690.1024973160210.0543195264012-0.009487849845460.248059122184-0.016228099810.1555014006952.322769099882.29965067858-28.1022386426
94.381780930381.749092025790.1636215509353.474233814510.6977242233321.35908656559-0.04416435838140.0195308496142-0.0431650230830.08422110800960.0961952957761-0.4048204025990.262253725070.673326441688-0.04541391039190.1206758630810.0288751959269-0.01567048596120.255641752314-0.01483719379280.1619844412891.536732050060.821631264611-20.3051241247
106.13148174639-5.184374760016.262327649365.31554220362-4.218834969427.626025600910.0989457568904-0.431962135042-0.5464543352830.4389354287870.2411465783960.3861890157520.76889352167-0.757960115929-0.3324980390190.272673950203-0.0311101536032-0.01009367805890.1749643478370.04335532041910.0997280308974-11.377180452-5.22100134901-13.6261194161
112.616273191130.709115823471-1.07114804821.708399719860.6936940618333.07885167468-0.0945898694697-0.1321263542110.3322205084820.429646368086-0.0871237418373-0.267504935179-0.1687643580590.1555533690050.1128712121420.133731735606-0.0283137873305-0.04741036799510.09497096861510.004725473059550.11508323043-7.152094344645.05886563353-8.78061401822
124.15232971916-2.0247140113-2.497380607554.53218722237-4.015688457689.23867431376-0.10865369401-0.126747184593-0.2429763482890.376398331610.0860121408109-0.2279139044220.205489362711-0.036182081660.02660938302990.125972937262-0.0179462563530.008953966061320.07912917000640.003533305625850.111460035181-16.52126517264.07754195882-10.9355750786
134.5513809442-3.77616734295-1.854488229014.542771620083.969876774674.956367963010.6148299813790.509238193662-0.569824814058-0.412603034042-0.3366018548410.3207554279810.415523430882-0.259802058581-0.2366156279810.226427394924-0.01393447154340.009615599274310.139900778648-0.01591808876790.201036543474-20.1609837549-1.64022421176-19.601078597
144.0766783231-0.393038508956-1.826410309897.409224948091.893037009325.89850650712-0.105252736497-0.193884013235-0.2137905726590.255155657259-0.009937658318410.03542492589120.422832189181-0.03376398080660.05682558601110.126531695795-0.0009663798174750.0361014767720.0805517737570.02164826895960.107785499143-21.96615386710.4332084512-9.95437556718
153.25851312371-1.90081424548-4.784043733164.132104657931.982830159079.10869848983-0.2670029312250.234785147602-0.0953389974885-0.61489055517-0.00260062106755-0.577506583138-0.2685575985840.5326922376920.3531586056510.227357351912-0.09573797768610.05481337993970.1871189189650.02037725089960.259891553928-9.2745117783826.5655118116-21.8782995738
166.956891900680.51846722608-2.652259077032.20634950002-0.1953040075583.1688493159-0.246190556576-0.163679429248-0.0801086777683-0.004249541183680.08328822527220.1668081148110.0848956179987-0.3665213627320.142096077940.106422350114-0.00613869193447-0.004738795168060.147492857558-0.0133450890770.0429581392873-35.392070432224.8419379425-9.10738723477
174.143164070412.7542434568-3.179690210576.57563831562-3.253685232066.0025931127-0.01486986709580.1714892221140.321496130742-0.03059556257080.193706761660.0764046969044-0.394279791677-0.0302573070449-0.1758800792030.1107370778420.00301656134467-0.02349013361850.1000667014830.007927579210470.111552471434-31.989667466233.7386032034-19.0457184082
185.92374012144-1.418957938491.829638306322.95823196962-0.9310026772532.4052019795-0.161738901803-0.07285623303090.4479398286270.1205245590810.119553528633-0.353613018228-0.2290613307630.1488221169920.02291268396590.0910714926894-0.00635836300712-0.002416281603250.0710966674454-0.02861265099210.0847164114105-17.009980924227.0160130627-9.28072656942
191.8010831499-0.948999086071-1.122647437951.097093256520.9808259210612.28373199671-0.0924751520765-0.07512208755660.0372651627190.137963524510.0534240672321-0.0062142508686-0.02370888558680.0145734279990.02815269673210.077740766048-0.00258392911445-0.003426025025390.05443927448280.006636716827020.0631992272167-24.771649748124.7208890647-8.6561745288
206.749159672364.707046577270.2921176317024.158452883362.356579758735.330173900160.1114149584640.5821425876740.799664700376-0.821308209605-0.0598865174282-0.475620772642-1.09748878569-0.531870478508-0.07777430056080.3783546873090.06120154862650.05350557480350.2081007925410.07538804155860.310813033157-17.046090898832.2292150659-31.0204124698
214.901003968750.816641200105-4.943978616741.99784595213-1.925875232617.376780429750.2044931876450.07814759283310.2726759372190.0356720299729-0.05191824871980.0656404209157-0.386401811764-0.117704378891-0.1591433781870.0827870356415-0.01002606624990.000923359610170.0814039273457-0.006181942539860.0804701860666-21.216847817823.8218576575-17.6515538304
224.052407965560.4666886351940.3958332615312.00009155334-1.971381594096.8086652442-0.0973382721467-0.1709958942920.06103332559410.190119295502-0.02070660328710.0472382287064-0.436509110941-0.5636969247230.09977304460350.127841327210.04496304515210.01901796544020.154372791210.004838256767270.0971102722841-36.506149690928.2539428083-0.307770808954
238.077565917321.2604447541-1.389295763896.04035579022-2.914900037912.4766479032-0.00221367799102-0.02363885973380.384929030253-0.2747014487350.147632203640.0506786869586-0.6840164085410.0913422170577-0.1608366904920.3683277127160.02710347618570.01880207100730.0942696540207-0.01334161085890.165595928103-29.366988933540.9335198451-8.78438206817
244.692694337950.8509777163780.5005725016644.101377978450.6644901091352.597221404570.0227258611768-0.06549438733870.476612196471-0.072457074314-0.1273633818930.0966078704994-0.432048424324-0.3096175840310.06522387857090.1778851810730.02961927257780.004778108902480.1343648696590.02729165368480.0971947806582-35.840645347232.8357293423-14.7205635534
253.97684425354.00242762703-3.821059265077.50363609102-4.89794849073.996595295330.100097396348-0.111231382368-0.118750742434-0.020711588660.2264565853320.0945798401360.196838354402-0.855002431189-0.3147638962830.157912841867-0.0194090164658-0.02292721139530.2498945817640.01501545637360.0914754898135-40.130297967826.0201762393-23.2412170847
260.645583465907-0.4358982810960.3113781069673.945994749221.085953515963.49204755016-0.05819114974490.42130440390.159174663288-0.2112043171930.068716053323-0.163165091404-0.1374525734840.0615522596262-0.01715590346190.0833152531429-0.0239051527438-0.000414080002210.1423180553860.05181638741620.110471202436-29.367122849927.2432577767-25.4086654285
277.56854978558-0.0220918793798-4.203909806846.916111801772.136137975367.307231253590.0156104759445-0.1336211550060.02129498965410.3175854638660.04349730682670.3444423775990.340888682452-0.249514913491-0.0401253035550.0590465781555-0.0161321665648-0.02811675977240.141987261477-0.02337805116180.112701356908-33.988344025716.2629498512-18.5250262622
287.68017460255-0.817683039919-2.049626267723.791190391892.142594374057.402190776020.01703659787230.2499784700620.0694566586617-0.191101127396-0.08480841070490.159141284989-0.0142901195927-0.3751080726560.01379735424380.0739055608364-0.000396179191022-0.02645784584430.113932056361-0.03289002659670.106998793518-24.672817853813.122647792-24.4512466881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:14)
2X-RAY DIFFRACTION2(chain A and resid 15:32)
3X-RAY DIFFRACTION3(chain A and resid 33:46)
4X-RAY DIFFRACTION4(chain A and resid 47:54)
5X-RAY DIFFRACTION5(chain A and resid 55:84)
6X-RAY DIFFRACTION6(chain A and resid 85:90)
7X-RAY DIFFRACTION7(chain A and resid 91:107)
8X-RAY DIFFRACTION8(chain A and resid 108:113)
9X-RAY DIFFRACTION9(chain A and resid 114:124)
10X-RAY DIFFRACTION10(chain A and resid 125:128)
11X-RAY DIFFRACTION11(chain A and resid 129:141)
12X-RAY DIFFRACTION12(chain A and resid 142:146)
13X-RAY DIFFRACTION13(chain A and resid 147:151)
14X-RAY DIFFRACTION14(chain A and resid 152:163)
15X-RAY DIFFRACTION15(chain B and resid 10:14)
16X-RAY DIFFRACTION16(chain B and resid 15:26)
17X-RAY DIFFRACTION17(chain B and resid 27:44)
18X-RAY DIFFRACTION18(chain B and resid 45:55)
19X-RAY DIFFRACTION19(chain B and resid 56:84)
20X-RAY DIFFRACTION20(chain B and resid 85:89)
21X-RAY DIFFRACTION21(chain B and resid 90:99)
22X-RAY DIFFRACTION22(chain B and resid 100:109)
23X-RAY DIFFRACTION23(chain B and resid 110:115)
24X-RAY DIFFRACTION24(chain B and resid 116:125)
25X-RAY DIFFRACTION25(chain B and resid 126:130)
26X-RAY DIFFRACTION26(chain B and resid 131:142)
27X-RAY DIFFRACTION27(chain B and resid 143:151)
28X-RAY DIFFRACTION28(chain B and resid 152:163)

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