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Structure-based design and synthesis of novel macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds as potent inhibitors of protein kinase CK2 and their anticancer activities
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PVJ PDB ENTRY 2PVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 297 14% PEG 4000, 0.05M Sodium Acetate, 0.10M TRISHCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.25 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.327 α = 90 b = 59.578 β = 103.419 c = 44.835 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 112 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2005-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 32.7 95 0.084 16.4 3.54 23749
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 92 0.409 2.5 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2PVJ 2 32.7 23749 22890 2284 91.6 0.19 0.228 RANDOM 26.2
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 5.09 1.683 -3.12 -1.97
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.96 c_scangle_it 2.9 c_scbond_it 2.02 c_angle_deg 1.91 c_mcangle_it 1.88 c_mcbond_it 1.25 c_improper_angle_d 0.71 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.96 c_scangle_it 2.9 c_scbond_it 2.02 c_angle_deg 1.91 c_mcangle_it 1.88 c_mcbond_it 1.25 c_improper_angle_d 0.71 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2734 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 27
Software Software Software Name Purpose MAR345dtb data collection CNX refinement DENZO data reduction SCALEPACK data scaling CNX phasing