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- PDB-7om1: Tankyrase 2 in complex with an inhibitor (OUL220) -

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Basic information

Entry
Database: PDB / ID: 7om1
TitleTankyrase 2 in complex with an inhibitor (OUL220)
Components(Poly [ADP-ribose] polymerase tankyrase- ...) x 2
KeywordsTRANSFERASE / Inhibitor / Enzyme
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Regulation of PTEN stability and activity / Wnt signaling pathway / protein polyubiquitination / nuclear envelope / positive regulation of canonical Wnt signaling pathway / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ankyrin repeat / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat ...Ankyrin repeat / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
8-methoxy-4~{H}-thieno[2,3-c]isoquinolin-5-one / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSowa, S.T. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063, 294085 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Analogs of TIQ-A as inhibitors of human mono-ADP-ribosylating PARPs.
Authors: Maksimainen, M.M. / Murthy, S. / Sowa, S.T. / Galera-Prat, A. / Rolina, E. / Heiskanen, J.P. / Lehtio, L.
History
DepositionMay 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 16, 2022Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_common_name
Revision 1.3Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Poly [ADP-ribose] polymerase tankyrase-2
A: Poly [ADP-ribose] polymerase tankyrase-2
BBB: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,85414
Polymers49,6924
Non-polymers1,16210
Water6,431357
1
AAA: Poly [ADP-ribose] polymerase tankyrase-2
A: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4277
Polymers24,8462
Non-polymers5815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-69 kcal/mol
Surface area10370 Å2
MethodPISA
2
BBB: Poly [ADP-ribose] polymerase tankyrase-2
B: Poly [ADP-ribose] polymerase tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4277
Polymers24,8462
Non-polymers5815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-69 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.210, 98.300, 118.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-1380-

HOH

21BBB-1364-

HOH

31B-1222-

HOH

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Components

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Poly [ADP-ribose] polymerase tankyrase- ... , 2 types, 4 molecules AAABBBAB

#1: Protein Poly [ADP-ribose] polymerase tankyrase-2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / Protein ...ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / Protein poly-ADP-ribosyltransferase tankyrase-2 / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-2 / TANK2 / Tankyrase-like protein / Tankyrase-related protein


Mass: 19482.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein/peptide Poly [ADP-ribose] polymerase tankyrase-2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / Protein ...ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / Protein poly-ADP-ribosyltransferase tankyrase-2 / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-2 / TANK2 / Tankyrase-like protein / Tankyrase-related protein


Mass: 5364.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 5 types, 367 molecules

#3: Chemical ChemComp-1OI / 8-methoxy-4~{H}-thieno[2,3-c]isoquinolin-5-one


Mass: 231.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris pH=8.5, 200mM Lithium Sulphate, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 58597 / % possible obs: 99.89 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 19.01
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 5791 / CC1/2: 0.817

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OWS

5ows


Resolution: 1.7→45.428 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.328 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1967 2930 5 %
Rwork0.1824 55667 -
all0.183 --
obs-58597 99.916 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-0.045 Å20 Å20 Å2
2---2.18 Å2-0 Å2
3---2.136 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 66 357 3768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133541
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173187
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.6434776
X-RAY DIFFRACTIONr_angle_other_deg1.2171.5817331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.78721.388209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09815581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2861527
X-RAY DIFFRACTIONr_chiral_restr0.0520.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02893
X-RAY DIFFRACTIONr_nbd_refined0.1840.2631
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.22998
X-RAY DIFFRACTIONr_nbtor_refined0.160.21651
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.21576
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2313
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.214
X-RAY DIFFRACTIONr_nbd_other0.1970.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.231
X-RAY DIFFRACTIONr_mcbond_it1.5243.1421695
X-RAY DIFFRACTIONr_mcbond_other1.523.141694
X-RAY DIFFRACTIONr_mcangle_it2.4724.6932118
X-RAY DIFFRACTIONr_mcangle_other2.4724.6952119
X-RAY DIFFRACTIONr_scbond_it1.8373.3571845
X-RAY DIFFRACTIONr_scbond_other1.8253.3451830
X-RAY DIFFRACTIONr_scangle_it2.9924.9482656
X-RAY DIFFRACTIONr_scangle_other2.9764.9282633
X-RAY DIFFRACTIONr_lrange_it5.04736.5424053
X-RAY DIFFRACTIONr_lrange_other4.93936.0893985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.332150.3134082X-RAY DIFFRACTION100
1.744-1.7920.2852090.2693982X-RAY DIFFRACTION100
1.792-1.8440.2812030.2563850X-RAY DIFFRACTION99.9753
1.844-1.9010.2451980.2273763X-RAY DIFFRACTION100
1.901-1.9630.2621910.2143642X-RAY DIFFRACTION99.9218
1.963-2.0320.2381870.1953550X-RAY DIFFRACTION99.9198
2.032-2.1080.1891780.183384X-RAY DIFFRACTION99.9158
2.108-2.1950.251730.1873286X-RAY DIFFRACTION100
2.195-2.2920.2211670.1783159X-RAY DIFFRACTION100
2.292-2.4040.2141590.1763023X-RAY DIFFRACTION99.9686
2.404-2.5340.211500.1772860X-RAY DIFFRACTION100
2.534-2.6880.2191440.1882735X-RAY DIFFRACTION99.8959
2.688-2.8730.2231350.1812556X-RAY DIFFRACTION100
2.873-3.1030.1741250.1792387X-RAY DIFFRACTION99.8013
3.103-3.3990.1791170.1782217X-RAY DIFFRACTION99.8716
3.399-3.80.1841050.1721998X-RAY DIFFRACTION99.6682
3.8-4.3870.153940.1451780X-RAY DIFFRACTION99.6809
4.387-5.3710.127790.1411512X-RAY DIFFRACTION99.562
5.371-7.5880.206640.21205X-RAY DIFFRACTION100

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