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- PDB-5ebt: Tankyrase 1 with Phthalazinone 2 -

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Basic information

Entry
Database: PDB / ID: 5ebt
TitleTankyrase 1 with Phthalazinone 2
ComponentsTankyrase-1
KeywordsTransferase/Transferase Inhibitor / Tankyrase / PARP / Centrosome clustering / oncology / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material ...negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / spindle assembly / mRNA transport / nuclear pore / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / mitotic spindle organization / TCF dependent signaling in response to WNT / Degradation of AXIN / peptidyl-threonine phosphorylation / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / protein transport / positive regulation of canonical Wnt signaling pathway / histone binding / peptidyl-serine phosphorylation / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / cell division / Golgi membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / 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 ...Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-5N8 / (R,R)-2,3-BUTANEDIOL / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24 Å
AuthorsKazmirski, S.L. / Johannes, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery of AZ0108, an orally bioavailable phthalazinone PARP inhibitor that blocks centrosome clustering.
Authors: Johannes, J.W. / Almeida, L. / Daly, K. / Ferguson, A.D. / Grosskurth, S.E. / Guan, H. / Howard, T. / Ioannidis, S. / Kazmirski, S. / Lamb, M.L. / Larsen, N.A. / Lyne, P.D. / Mikule, K. / ...Authors: Johannes, J.W. / Almeida, L. / Daly, K. / Ferguson, A.D. / Grosskurth, S.E. / Guan, H. / Howard, T. / Ioannidis, S. / Kazmirski, S. / Lamb, M.L. / Larsen, N.A. / Lyne, P.D. / Mikule, K. / Ogoe, C. / Peng, B. / Petteruti, P. / Read, J.A. / Su, N. / Sylvester, M. / Throner, S. / Wang, W. / Wang, X. / Wu, J. / Ye, Q. / Yu, Y. / Zheng, X. / Scott, D.A.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tankyrase-1
B: Tankyrase-1
C: Tankyrase-1
D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,02114
Polymers96,5624
Non-polymers2,46010
Water6,810378
1
A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8004
Polymers24,1401
Non-polymers6603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7103
Polymers24,1401
Non-polymers5702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8004
Polymers24,1401
Non-polymers6603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7103
Polymers24,1401
Non-polymers5702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.733, 151.189, 57.224
Angle α, β, γ (deg.)90.000, 96.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tankyrase-1 / TANK1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / Poly [ADP-ribose] polymerase 5A / ...TANK1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / Poly [ADP-ribose] polymerase 5A / TNKS-1 / TRF1-interacting ankyrin-related ADP-ribose polymerase / Tankyrase I


Mass: 24140.432 Da / Num. of mol.: 4 / Fragment: UNP residue 1106-1314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95271, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-5N8 / 4-[bis(fluoranyl)-[3-[[(6~{S})-6-methyl-3-(trifluoromethyl)-6,8-dihydro-5~{H}-[1,2,4]triazolo[4,3-a]pyrazin-7-yl]carbonyl]phenyl]methyl]-2~{H}-phthalazin-1-one


Mass: 504.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H17F5N6O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 14% PEG 20K, 0.1 M PCPT pH5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.24→151.189 Å / Num. all: 43852 / Num. obs: 43852 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.81 Å2 / Rpim(I) all: 0.075 / Rrim(I) all: 0.146 / Rsym value: 0.107 / Net I/av σ(I): 6.409 / Net I/σ(I): 9.6 / Num. measured all: 161397
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.24-2.363.50.4711.52245863990.3280.4713.298.9
2.36-2.513.60.371.92173160420.2550.37499.3
2.51-2.683.70.2792.52087056830.190.2795.199.4
2.68-2.893.80.1943.72007253400.130.1946.999.7
2.89-3.173.80.1275.61857148870.0850.1279.499.6
3.17-3.543.80.0838.51651543830.0570.0831399.1
3.54-4.093.70.06111.81464939130.0410.06116.799.2
4.09-5.013.70.04913.11215632830.0330.0492098.7
5.01-7.093.70.04713.8952525410.0320.04719.498.5
7.09-151.1893.50.04313.9485013810.0310.04320.996.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.76 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.99 Å
Translation2.5 Å27.99 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASER2.1.4phasing
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→18.35 Å / Cor.coef. Fo:Fc: 0.9235 / Cor.coef. Fo:Fc free: 0.8978 / SU R Cruickshank DPI: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.266 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 2206 5.04 %RANDOM
Rwork0.171 ---
obs0.1729 43744 98.79 %-
Displacement parametersBiso max: 137.06 Å2 / Biso mean: 30.05 Å2 / Biso min: 5.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.7322 Å20 Å2-7.667 Å2
2---4.7941 Å20 Å2
3---2.0619 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: final / Resolution: 2.24→18.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6723 0 160 378 7261
Biso mean--18.7 32.41 -
Num. residues----832
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2497SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1173HARMONIC5
X-RAY DIFFRACTIONt_it7087HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONI5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion856SEMIHARMONI5
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_contact7994SEMIHARMONI4
X-RAY DIFFRACTIONt_bond_d7087HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg9560HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion18.51
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2374 167 5.29 %
Rwork0.1936 2988 -
all0.1959 3155 -
obs--98.79 %

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