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Discovery of SMD-3236, a Potent, Highly Selective and Efficacious SMARCA2 Degrader for the Treatment of SMARC4-Deficient Human Cancers
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 75TP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 281.15 0.25 M Calcium acetate
0.1 M Sodium cacodylate pH 5.5
8% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.91 57.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.13 α = 90 b = 132.01 β = 90 c = 210.7 γ = 90
Symmetry Space Group C 2 2 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 2023-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000 SPring-8 BL45XU
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 3.3 48.1 100 0.285 0.296 0.079 0.994 10.4 13.5 19935
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 3.3 3.56 100 1.2 1.248 0.342 0.812 13.1
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 (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 3.3 48.1 18919 1014 99.93 0.21124 0.20734 0.2096 0.28581 0.2897 RANDOM 78.343
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] -0.14 0.55 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.6 r_long_range_B_refined 15.952 r_long_range_B_other 15.951 r_scangle_other 11.46 r_mcangle_it 11.374 r_mcangle_other 11.373 r_dihedral_angle_1_deg 8.004 r_dihedral_angle_2_deg 7.539 r_mcbond_it 7.171 r_mcbond_other 7.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.6 r_long_range_B_refined 15.952 r_long_range_B_other 15.951 r_scangle_other 11.46 r_mcangle_it 11.374 r_mcangle_other 11.373 r_dihedral_angle_1_deg 8.004 r_dihedral_angle_2_deg 7.539 r_mcbond_it 7.171 r_mcbond_other 7.171 r_scbond_it 7.089 r_scbond_other 7.088 r_angle_refined_deg 1.385 r_angle_other_deg 0.43 r_chiral_restr 0.062 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7272 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing