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Discovery of an Orally Bioavailable KRAS G12D Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Sodium acetate, pH 4.6,30% PEG 4000 and 0.2M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.175 α = 90 b = 53.63 β = 90 c = 90.206 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 100 PIXEL DECTRIS PILATUS 6M 2020-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.35 53.63 99.5 0.04 0.04 0.01 1 26.4 12.6 43420 12.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 95.4 0.3 0.32 0.1 0.96 3.7 9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.35 46.099 43359 2120 99.404 0.155 0.1535 0.1614 0.1782 0.1816 18.98
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] -0.038 -0.598 0.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.85 r_dihedral_angle_6_deg 16.356 r_lrange_it 12.6 r_lrange_other 11.988 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_other_2_deg 7.628 r_scangle_it 6.462 r_scangle_other 6.46 r_dihedral_angle_1_deg 5.968 r_mcangle_it 4.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.85 r_dihedral_angle_6_deg 16.356 r_lrange_it 12.6 r_lrange_other 11.988 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_other_2_deg 7.628 r_scangle_it 6.462 r_scangle_other 6.46 r_dihedral_angle_1_deg 5.968 r_mcangle_it 4.722 r_mcangle_other 4.72 r_scbond_it 4.508 r_scbond_other 4.506 r_rigid_bond_restr 4.052 r_mcbond_it 3.077 r_mcbond_other 3.076 r_angle_refined_deg 2.007 r_angle_other_deg 1.104 r_nbd_other 0.216 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.173 r_symmetry_nbd_other 0.148 r_chiral_restr 0.115 r_symmetry_xyhbond_nbd_refined 0.115 r_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.069 r_gen_planes_refined 0.016 r_bond_refined_d 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1371 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing