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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 5.2 293 0.8 M trisodium citrate, 0.1 M citrate, pH 5.2, Silver Bullets Bio B12 (0.025% thymidine-5'-triphosphate sodium salt, 0.025% alpha-ketoglutaric acid disodium salt, 0.025% 2-nitrophenyl beta-D-galactopyranoside, 0.025% cis-aconitic acid, 0.002 M HEPES sodium, pH 6.8)
Crystal Properties Matthews coefficient Solvent content 4.09 69.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.171 α = 90 b = 146.438 β = 97.13 c = 111.3 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 2011-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97648 ALS 5.0.2
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 3.3 50 99.9 0.147 5.9 4.2 42899
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 3.3 3.36 99.6 0.89 4.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2F2U 3.3 25 40630 2150 98.62 0.2073 0.2058 0.2357 0.218 RANDOM 87.372
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] 4.35 5.36 -7.03 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.256 r_dihedral_angle_4_deg 23.253 r_dihedral_angle_3_deg 20.25 r_dihedral_angle_1_deg 8.07 r_angle_refined_deg 1.327 r_angle_other_deg 1.142 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.256 r_dihedral_angle_4_deg 23.253 r_dihedral_angle_3_deg 20.25 r_dihedral_angle_1_deg 8.07 r_angle_refined_deg 1.327 r_angle_other_deg 1.142 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12282 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing