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Discovery of a Novel, Highly Potent, and Selective Thieno[3,2-d]pyrimidinone-Based Cdc7 inhibitor with a Quinuclidine Moiety (TAK-931) as an Orally Active Investigational Anti-Tumor Agent
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F2U PDB entry 2F2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 293 0.8 M trisodium citrate, 0.1 M citrate, pH 5.1
Crystal Properties Matthews coefficient Solvent content 4.01 69.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.456 α = 90 b = 146.416 β = 97.12 c = 111.876 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 ADSC QUANTUM 315r 2011-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
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 2.65 50 99.9 0.103 9.1 4.2 83024
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 2.65 2.7 99.3 0.788 3.9
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 2F2U 2.65 25 78660 4128 99.05 0.195 0.1934 0.194 0.225 0.2231 RANDOM 57.52
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] 2.15 3.07 -2.38 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.593 r_dihedral_angle_4_deg 24.358 r_dihedral_angle_3_deg 16.831 r_dihedral_angle_1_deg 7.168 r_angle_refined_deg 1.328 r_angle_other_deg 1.175 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.593 r_dihedral_angle_4_deg 24.358 r_dihedral_angle_3_deg 16.831 r_dihedral_angle_1_deg 7.168 r_angle_refined_deg 1.328 r_angle_other_deg 1.175 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12694 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing