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Discovery of a Novel Class of triazolones as Checkpoint Kinase Inhibitors - Hit to Lead Exploration
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X8D PDB ENTRY 2X8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 HANGING DROP 3UL PLUS 3UL PROTEIN: 7 MG/ML, 25MM TRIS PH7.5, 500MM NACL, 5% GLYCEROL, 5MM DTT, 2MM COMPOUND WELL: 12-16% (W/V) PEG3350, 100-200MM AMMONIUM SULPHATE, 2% (V/V) GLYCEROL AND 100 MM SODIUM CACODYLATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.48 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.055 α = 90 b = 65.858 β = 101.73 c = 54.468 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH SX-165 2002-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2.5 16.55 72.5 0.11 5.4 2.6 7559 2
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) 1 2.5 2.64 26.3 0.27 2 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2X8D 2.5 16.51 7187 372 69.68 0.23547 0.23185 0.242 0.30865 0.322 RANDOM 42.257
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] -3.33 1.81 1.97 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.042 r_dihedral_angle_4_deg 21.374 r_dihedral_angle_3_deg 18.202 r_dihedral_angle_1_deg 6.776 r_scangle_it 1.982 r_angle_refined_deg 1.531 r_scbond_it 1.223 r_mcangle_it 0.951 r_angle_other_deg 0.93 r_mcbond_it 0.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.042 r_dihedral_angle_4_deg 21.374 r_dihedral_angle_3_deg 18.202 r_dihedral_angle_1_deg 6.776 r_scangle_it 1.982 r_angle_refined_deg 1.531 r_scbond_it 1.223 r_mcangle_it 0.951 r_angle_other_deg 0.93 r_mcbond_it 0.516 r_mcbond_other 0.079 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2054 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing