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- PDB-5ece: Tankyrase 1 with Phthalazinone 1 -

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Basic information

Entry
Database: PDB / ID: 5ece
TitleTankyrase 1 with Phthalazinone 1
ComponentsTankyrase-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Tankyrase / Inhibitor / 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 / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / 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 / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / mRNA transport / spindle assembly / 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 / positive regulation of canonical Wnt signaling pathway / protein transport / 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 / cytosol / cytoplasm
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-5N2 / ACETATE ION / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsKazmirski, S.L. / Johannes, J. / Read, J.A. / Howard, T. / Larsen, N.A. / Ferguson, A.D.
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 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: 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 / database_2 / pdbx_struct_oper_list
Item: _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

Downloads & links

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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)99,32919
Polymers97,2224
Non-polymers2,10715
Water6,269348
1
A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8844
Polymers24,3061
Non-polymers5783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9465
Polymers24,3061
Non-polymers6404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9435
Polymers24,3061
Non-polymers6374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5575
Polymers24,3061
Non-polymers2524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.970, 59.980, 77.190
Angle α, β, γ (deg.)86.210, 78.890, 89.060
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 24305.559 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 363 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-5N2 / 2-[4-[3-[(4-oxidanylidene-3~{H}-phthalazin-1-yl)methyl]phenyl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile


Mass: 450.492 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H22N6O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG 3350, 0.1 M MES pH 6.5, 0.2 Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.684→75.593 Å / Num. all: 47363 / Num. obs: 47363 / % possible obs: 96.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 34.76 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.114 / Rrim(I) all: 0.161 / Rsym value: 0.114 / Net I/av σ(I): 1.753 / Net I/σ(I): 7.1 / Num. measured all: 90715
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.321.90.5180.61200063860.5180.518289.5
2.32-2.461.90.3621.31285465930.3620.3622.697.5
2.46-2.631.90.2652.11221762710.2650.2653.597.7
2.63-2.841.90.2121.41124457790.2120.2124.797.8
2.84-3.111.90.1364.61033553350.1360.1366.598
3.11-3.481.90.11.9933048490.10.19.598.3
3.48-4.021.90.0821.5812342610.0820.08212.598.3
4.02-4.921.90.0598.4680136070.0590.05915.398.2
4.92-6.961.80.0569495227640.0560.05614.697.2
6.96-75.5931.90.0539.2285915180.0530.05317.698

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Processing

Software
NameVersionClassification
SCALA3.2.21data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.2→44 Å / Cor.coef. Fo:Fc: 0.9404 / Cor.coef. Fo:Fc free: 0.9125 / SU R Cruickshank DPI: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 2366 5 %RANDOM
Rwork0.1812 ---
obs0.1833 47321 96.59 %-
Displacement parametersBiso max: 137.82 Å2 / Biso mean: 37.93 Å2 / Biso min: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.1217 Å22.7849 Å2-0.2022 Å2
2---0.8985 Å20.2808 Å2
3---1.0202 Å2
Refine analyzeLuzzati coordinate error obs: 0.274 Å
Refinement stepCycle: final / Resolution: 2.2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 138 348 7041
Biso mean--54.98 37.75 -
Num. residues----812
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2420SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes165HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1013HARMONIC5
X-RAY DIFFRACTIONt_it6871HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion836SEMIHARMONIC5
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_contact7111SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6871HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9230HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion17.61
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2588 150 5.09 %
Rwork0.214 2797 -
all0.2163 2947 -
obs--81.85 %
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)
11.43320.8847-0.12151.42930.02540.8756-0.04790.0126-0.047-0.00860.0773-0.0270.03330.0205-0.0293-0.04-0.12660.016-0.03860.0029-0.169110.545-3.93836.441
20.91180.80750.18121.49840.22281.26610.0335-0.11150.1413-0.0171-0.06710.0931-0.0831-0.11270.0337-0.0556-0.1070.0202-0.016-0.012-0.172521.86-19.0153.12
31.64460.94530.32831.56180.07211.0029-0.0052-0.0402-0.06690.0065-0.0120.04110.0373-0.02230.0172-0.0379-0.10460.0236-0.0460.0029-0.164626.328-29.43839.343
41.92611.7499-0.28222.7244-0.40021.0543-0.15050.091-0.0773-0.31480.0924-0.0060.0663-0.04740.0581-0.0324-0.14030.016-0.04390.0232-0.1549-0.0060.0840.303
51.30330.4295-0.60371.613-0.23021.55080.04790.0049-0.11690.0237-0.0204-0.22910.0103-0.0878-0.0276-0.0395-0.1155-0.04170.07340.04660.104322.025-18.00927.498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1104 - A|1316 }A1104 - 1316
2X-RAY DIFFRACTION2{ B|1104 - B|1314 }B1104 - 1314
3X-RAY DIFFRACTION3{ C|1104 - C|1315 }C1104 - 1315
4X-RAY DIFFRACTION4{ D|1104 - D|1316 }D1104 - 1316
5X-RAY DIFFRACTION5{ A|1402 - A|1402 C|1403 - C|1403 B|1403 - B|1403 }A1402
6X-RAY DIFFRACTION5{ A|1402 - A|1402 C|1403 - C|1403 B|1403 - B|1403 }C1403
7X-RAY DIFFRACTION5{ A|1402 - A|1402 C|1403 - C|1403 B|1403 - B|1403 }B1403

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