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- PDB-5al3: Crystal structure of TNKS2 in complex with 2-(2,4-dichlorophenyl)... -

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Basic information

Entry
Database: PDB / ID: 5al3
TitleCrystal structure of TNKS2 in complex with 2-(2,4-dichlorophenyl)-1- methyl-1H,2H,3H,4H-pyrido(2,3-d)pyrimidin-4-one
ComponentsTANKYRASE 2
KeywordsTRANSFERASE / PROTEIN-LIGAND COMPLEX / DIPHTHERIA TOXIN LIKE FOLD / ADP- RIBOSYLATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / 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 / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / 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 / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / 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 / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 ...Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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-TGW / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNkizinkiko, Y. / Lehtio, L.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: Discovery of Potent and Selective Nonplanar Tankyrase Inhibiting Nicotinamide Mimics.
Authors: Nkizinkiko, Y. / Suneel Kumar, B.V.S. / Jeankumar, V.U. / Haikarainen, T. / Koivunen, J. / Madhuri, C. / Yogeeswari, P. / Venkannagari, H. / Obaji, E. / Pihlajaniemi, T. / Sriram, D. / Lehtio, L.
History
DepositionMar 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 2
B: TANKYRASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,09914
Polymers54,6002
Non-polymers1,50012
Water5,927329
1
A: TANKYRASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1428
Polymers27,3001
Non-polymers8427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TANKYRASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9586
Polymers27,3001
Non-polymers6585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.620, 98.570, 118.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2091-

HOH

21B-2083-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TANKYRASE 2 / TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / POLY ADP-RIBOSE POLYMERASE 5B / TNKS-2 / ...TANK2 / ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6 / POLY ADP-RIBOSE POLYMERASE 5B / TNKS-2 / TRF1-INTERACTING ANKYRIN -RELATED ADP-RIBOSE POLYMERASE 2 / TANKYRASE II / TANKYRASE-LIKE PROTEIN / TANKYRASE-RELATED PROTEIN / ARTD6


Mass: 27299.764 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 946-1162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase

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Non-polymers , 5 types, 341 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TGW / (2R)-2-(2,4-dichlorophenyl)-1-methyl-2,3-dihydropyrido[2,3-d]pyrimidin-4-one


Mass: 308.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11Cl2N3O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2013
RadiationMonochromator: WATER-COOLED SI(111) DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 53428 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.34 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U9H

3u9h


Resolution: 1.75→29.81 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.045 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19309 2672 5 %RANDOM
Rwork0.15873 ---
obs0.16045 50756 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.239 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.94 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 86 329 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193564
X-RAY DIFFRACTIONr_bond_other_d0.0010.023279
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9554810
X-RAY DIFFRACTIONr_angle_other_deg0.7863.0027531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77322.896183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41815589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4111529
X-RAY DIFFRACTIONr_chiral_restr0.0890.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024073
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8062.3321683
X-RAY DIFFRACTIONr_mcbond_other1.8052.3311682
X-RAY DIFFRACTIONr_mcangle_it2.73.482102
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7232.7131880
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 194 -
Rwork0.224 3683 -
obs--98.58 %

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