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- PDB-9ysi: Covalent allosteric inhibitor of human DNA polymerase theta -

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Basic information

Entry
Database: PDB / ID: 9ysi
TitleCovalent allosteric inhibitor of human DNA polymerase theta
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
  • DNA polymerase theta
KeywordsDNA/TRANSFERASE/INHIBITOR / inhibitor / complex / DNA BINDING PROTEIN / DNA-TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / DNA synthesis involved in DNA repair / replication fork processing / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes ...double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / DNA synthesis involved in DNA repair / replication fork processing / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes / site of DNA damage / DNA helicase activity / protein homooligomerization / base-excision repair / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA-directed DNA polymerase / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA repair / chromatin binding / DNA damage response / magnesium ion binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
: / : / DNA_pol_Q helicase like region helical domain / Domain of unknown function (DUF7898) / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...: / : / DNA_pol_Q helicase like region helical domain / Domain of unknown function (DUF7898) / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMader, P. / Sicheri, F.
Funding support Canada, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
Canadian Institutes of Health Research (CIHR)PJT-178026 Canada
Canadian Institutes of Health Research (CIHR)PJT-186218 Canada
Canadian Institutes of Health Research (CIHR)PJT-180338 Canada
Other privateTFRI 1107-04 Canada
Citation
Journal: Acs Med.Chem.Lett. / Year: 2026
Title: Design of a Targeted Covalent Probe to Interrogate the DNA Polymerase Activity of Pol theta.
Authors: Bubenik, M. / Mader, P. / Orlicky, S. / Perryman, A.L. / Hamel, M. / Godbout, C. / Falgueyret, J.P. / Kurinov, I. / Wong, C. / Gingras, A.C. / Mamane, Y. / Zinda, M. / Morris, S.J. / ...Authors: Bubenik, M. / Mader, P. / Orlicky, S. / Perryman, A.L. / Hamel, M. / Godbout, C. / Falgueyret, J.P. / Kurinov, I. / Wong, C. / Gingras, A.C. / Mamane, Y. / Zinda, M. / Morris, S.J. / Gallant, M. / Sfeir, A. / Black, W.C. / Durocher, D. / Zimmermann, M. / Sicheri, F.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase theta
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
D: DNA polymerase theta
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')
F: DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,58521
Polymers168,7126
Non-polymers2,87315
Water16,069892
1
A: DNA polymerase theta
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,90413
Polymers84,3563
Non-polymers1,54810
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-67 kcal/mol
Surface area30260 Å2
MethodPISA
2
D: DNA polymerase theta
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')
F: DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6818
Polymers84,3563
Non-polymers1,3255
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-18 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.522, 66.621, 151.914
Angle α, β, γ (deg.)90.000, 122.229, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase theta / DNA polymerase eta


Mass: 75200.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: engineered construct, 5 surface loops are truncated, AA 1868-1888, 1921-1933, 2149-2172, 2264-2303, and 2516-2523
Source: (gene. exp.) Homo sapiens (human) / Gene: POLQ, POLH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75417, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')


Mass: 5157.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')


Mass: 3998.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 907 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-A1CZ4 / N-(4-{2-[2,4-bis(trifluoromethyl)phenyl]-N-phenylacetamido}but-2-yn-1-yl)-2-(ethanesulfonamido)benzamide


Mass: 625.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H25F6N3O4S / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 3350, 200 mM sodium-potassium tartrate, 3% glycerol, 0.02% sucrose monolaurate, and 20 mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.997→60.97 Å / Num. obs: 485652 / % possible obs: 97.77 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.95 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.05461 / Rpim(I) all: 0.03429 / Rrim(I) all: 0.0647 / Net I/σ(I): 13.85
Reflection shellResolution: 2→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 12898 / CC1/2: 0.539 / CC star: 0.837 / Rpim(I) all: 0.6324 / Rrim(I) all: 1.173 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→60.97 Å / SU ML: 0.2329 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 7048 5.04 %
Rwork0.1754 132749 -
obs0.1772 139797 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.6 Å2
Refinement stepCycle: LAST / Resolution: 2→60.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9938 950 182 892 11962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015911371
X-RAY DIFFRACTIONf_angle_d1.36115612
X-RAY DIFFRACTIONf_chiral_restr0.08121753
X-RAY DIFFRACTIONf_plane_restr0.01381834
X-RAY DIFFRACTIONf_dihedral_angle_d21.03524242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.35862080.31314030X-RAY DIFFRACTION89.01
2.02-2.040.31862240.27374417X-RAY DIFFRACTION98.24
2.04-2.070.26242290.25084409X-RAY DIFFRACTION98.53
2.07-2.090.27862580.24134382X-RAY DIFFRACTION98.39
2.09-2.120.27782200.22844430X-RAY DIFFRACTION98.31
2.12-2.150.24922180.21944516X-RAY DIFFRACTION98.36
2.15-2.180.25392430.21734397X-RAY DIFFRACTION98.53
2.18-2.210.27952490.21284455X-RAY DIFFRACTION98.64
2.21-2.250.27452390.22184374X-RAY DIFFRACTION98.48
2.25-2.290.25172450.22064415X-RAY DIFFRACTION98.02
2.29-2.330.24292040.20124360X-RAY DIFFRACTION96.94
2.33-2.370.22822300.19734500X-RAY DIFFRACTION98.85
2.37-2.410.26112360.1974430X-RAY DIFFRACTION98.94
2.41-2.460.22622290.18584488X-RAY DIFFRACTION98.91
2.46-2.520.23032490.18554432X-RAY DIFFRACTION98.76
2.52-2.570.23032130.17654485X-RAY DIFFRACTION98.39
2.57-2.640.21472540.17374392X-RAY DIFFRACTION98.41
2.64-2.710.23042610.18144419X-RAY DIFFRACTION98.67
2.71-2.790.2452240.18694435X-RAY DIFFRACTION97.47
2.79-2.880.24832430.19224377X-RAY DIFFRACTION97.3
2.88-2.980.24112300.1914470X-RAY DIFFRACTION98.97
2.98-3.10.20762500.19084467X-RAY DIFFRACTION98.7
3.1-3.240.21712250.17674507X-RAY DIFFRACTION98.89
3.24-3.420.21822180.16734460X-RAY DIFFRACTION98.48
3.42-3.630.20132620.16974416X-RAY DIFFRACTION97.6
3.63-3.910.16762400.14784417X-RAY DIFFRACTION96.42
3.91-4.30.16332520.13684440X-RAY DIFFRACTION98.1
4.3-4.920.18032310.13434466X-RAY DIFFRACTION97.37
4.93-6.20.17592370.16584415X-RAY DIFFRACTION96.1
6.2-60.970.20022270.17414548X-RAY DIFFRACTION95.61
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)
13.143080792330.620524421658-0.3447514323294.58881616064-1.098611689443.383861116260.003390668396240.4481876028130.100443600186-0.2147846736870.0895594114085-0.152039494961-0.02878692033820.508331623512-0.07712845399680.176458956735-0.01308231612110.02184806778560.433061614385-0.07002130175430.24993186830759.0809493888-10.859054440815.7902235855
22.20280390699-0.633665281762-0.2067925364440.7648530763320.1723411770332.77904001893-0.0118429358270.0179581206812-0.1003453698620.04017250258950.029330806762-0.1015425838590.04026667394960.533099116745-0.01659560485740.202710936689-0.01902340915460.003209266935910.238162958265-0.03205824947140.25308272982752.9229889668-9.6268378325430.7900437864
30.435949305863-0.165415966359-0.1688413774690.8756954997070.3721351275340.5522868848850.000824668932612-0.0003177661192180.0721708419677-0.009749521682760.01227808038720.018209600901-0.1395494796930.0147307942987-0.01266949747580.235846258192-0.01793989781270.01303476174160.1623878496370.003535861654520.23352073339532.2032529877.0966373000148.4629296161
40.2848385304340.375270359022-0.4224464969683.4406534438-1.574614691563.523155385770.0260476775188-0.1193958051460.708769327972-0.01257475021570.0595084785582-0.615991387378-0.5129753309360.507871309421-0.04565326209870.372245629056-0.1016788558150.06884274172830.430835878838-0.06312319027110.62841554351347.915149405114.273664459254.3994975159
53.795793815021.134176374820.8912389117840.474564083031-0.3194069817712.77802357224-0.3599928468150.03501029611890.333617813971-0.6509329072830.230138954571-1.20767348686-0.471000237230.9452202888550.1827559852690.478283924619-0.1246829136320.1869027926140.540770433991-0.06725081694261.0126612941748.136113539917.531461808149.7841788648
63.272989253890.7189342602450.3881714571252.2721034713-0.9473924856034.286759232110.07193588889140.186041196666-0.221846634353-0.284846186275-0.123555237816-0.1105947776780.2870822501310.3257056071860.02954800203310.2255282783310.0087770217621-0.009311175702730.5329770824560.08818559191370.320639763075-44.1823263573-26.78992587324.87638664994
72.884444212071.25655489420.2943530230091.04928899704-0.1007148447920.5383327161140.03496489517050.08030281420750.01519830524430.193391234583-0.220475353978-0.0991213591869-0.06978823336350.5557950581670.139780167960.288916543586-0.0842185200432-0.06787256317030.7839327374460.1656605045930.364967174796-34.7548382032-23.078501009219.2083402494
81.02260051566-0.1034837986870.6348557684930.1378311218070.06337634739540.527403779978-0.2597508493391.270195767480.0800198318516-0.05296252265340.164783868590.104756423920.207302848518-0.110791427475-0.1882577694590.402365927991-0.237112610076-0.08470899270331.153064281030.1712614009350.4521191635423.50671317454-20.213484312319.6692176205
90.967865447404-0.05473841577150.3288806029430.3178052421710.550282155421.08326269184-0.3210369658870.5144180049680.661182145938-0.0916236038740.1485010447580.0512112261716-0.5350777414240.4412005181290.1605610685290.528277896855-0.275803404298-0.2457082124890.8650513169750.3169273109940.711421994174-15.2301609512-3.8607849116228.383158419
100.9334223877310.462363769287-0.5774153736460.7024086064841.354247841555.98757763611-0.0417868262561-0.116166028497-0.5546317557020.4773507813050.167775503263-0.4256013730360.9234879258680.752308422853-0.1123810571270.490473834161-0.0111684885455-0.1780817760780.7697962118290.1423035305080.673858332462-8.99545352269-23.852061688533.7597108096
115.04320814087-2.777497312090.05460625204683.409036638611.624309984055.636980639590.144385882923-0.52315809485-0.8445710057681.00697202538-0.323034297955-0.1754351562951.028866768880.03972834863670.04892754156910.733819860648-0.364730642042-0.2177663196251.162794413840.3071053830160.812821840492-6.31384563901-22.331601798530.1840178111
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 90 )AA7 - 901 - 84
22chain 'A' and (resid 91 through 245 )AA91 - 24585 - 239
33chain 'A' and (resid 246 through 668 )AA246 - 668240 - 653
44chain 'B' and (resid 1 through 15 )BB1 - 15
55chain 'C' and (resid 3 through 13 )CC3 - 13
66chain 'D' and (resid 4 through 116 )DD4 - 1161 - 113
77chain 'D' and (resid 117 through 245 )DD117 - 245114 - 242
88chain 'D' and (resid 246 through 419 )DD246 - 419243 - 408
99chain 'D' and (resid 420 through 666 )DD420 - 666409 - 649
1010chain 'E' and (resid 1 through 13 )EE1 - 13
1111chain 'F' and (resid 6 through 13 )FF6 - 13

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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