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- PDB-4li7: TANKYRASE-1 complexed with small molecule inhibitor 4-chloro-5-cy... -

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Basic information

Entry
Database: PDB / ID: 4li7
TitleTANKYRASE-1 complexed with small molecule inhibitor 4-chloro-5-cyano-N-{2-[4-(4-fluorobenzoyl)piperidin-1-yl]ethyl}-2-methoxybenzamide
ComponentsTankyrase-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / 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-1XP / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER METHODS / Resolution: 2.2 Å
AuthorsKirby, C.A. / Stams, T.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Identification of NVP-TNKS656: The Use of Structure-Efficiency Relationships To Generate a Highly Potent, Selective, and Orally Active Tankyrase Inhibitor.
Authors: Shultz, M.D. / Cheung, A.K. / Kirby, C.A. / Firestone, B. / Fan, J. / Chen, C.H. / Chen, Z. / Chin, D.N. / Dipietro, L. / Fazal, A. / Feng, Y. / Fortin, P.D. / Gould, T. / Lagu, B. / Lei, H. ...Authors: Shultz, M.D. / Cheung, A.K. / Kirby, C.A. / Firestone, B. / Fan, J. / Chen, C.H. / Chen, Z. / Chin, D.N. / Dipietro, L. / Fazal, A. / Feng, Y. / Fortin, P.D. / Gould, T. / Lagu, B. / Lei, H. / Lenoir, F. / Majumdar, D. / Ochala, E. / Palermo, M.G. / Pham, L. / Pu, M. / Smith, T. / Stams, T. / Tomlinson, R.C. / Toure, B.B. / Visser, M. / Wang, R.M. / Waters, N.J. / Shao, W.
History
DepositionJul 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,23411
Polymers50,8192
Non-polymers1,4149
Water3,279182
1
A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1656
Polymers25,4101
Non-polymers7555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0695
Polymers25,4101
Non-polymers6594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.400, 44.000, 87.400
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number5
Space group name H-MC121

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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: 25409.711 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP residues 1105-1325
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-1XP / 4-chloro-5-cyano-N-{2-[4-(4-fluorobenzoyl)piperidin-1-yl]ethyl}-2-methoxybenzamide


Mass: 443.898 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23ClFN3O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONFLICT M1266I PRESENT IN UNP ENTRY O95271

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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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 17% PEG 3350, 100mM bis-tris, pH 6.2, 100 mM Ammonium Sulfate, 9 mg/ml TNKS1, 1 mM inhibitor, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.2→50 Å / Num. obs: 22921 / % possible obs: 93.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5.12 / % possible all: 69.5

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Processing

Software
NameClassification
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
RefinementMethod to determine structure: FOURIER METHODS / Resolution: 2.2→43.7 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.251 1071 -
Rwork0.194 --
obs-22084 90.5 %
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.83 Å20 Å2-2.97 Å2
2--14.79 Å20 Å2
3----9.96 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 89 182 3565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.5
X-RAY DIFFRACTIONf_dihedral_angle_d24.4
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.286 120 -
Rwork0.228 --
obs-2616 68.1 %

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