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Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and orally active factor Xa inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EZQ PDB ENTRY 1EZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25.% .PEG 3350, 0.1M .tris pH 8.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.002 α = 90 b = 70.345 β = 90 c = 78.546 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD 2009-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.45 50 99.3 48381 19.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 99.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EZQ 1.45 35.17 45527 2419 98.81 0.19503 0.19414 0.21169 0.2518 RANDOM 14.669
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] 0.05 0.34 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.711 r_dihedral_angle_4_deg 15.141 r_dihedral_angle_3_deg 12.928 r_dihedral_angle_1_deg 5.938 r_scangle_it 2.443 r_scbond_it 1.634 r_angle_refined_deg 1.147 r_mcangle_it 1.071 r_mcbond_it 0.652 r_symmetry_metal_ion_refined 0.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.711 r_dihedral_angle_4_deg 15.141 r_dihedral_angle_3_deg 12.928 r_dihedral_angle_1_deg 5.938 r_scangle_it 2.443 r_scbond_it 1.634 r_angle_refined_deg 1.147 r_mcangle_it 1.071 r_mcbond_it 0.652 r_symmetry_metal_ion_refined 0.368 r_nbtor_refined 0.303 r_metal_ion_refined 0.261 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.09 r_chiral_restr 0.08 r_symmetry_hbond_refined 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2203 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement