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Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 300 PEG 6k
Crystal Properties Matthews coefficient Solvent content 1.97 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.302 α = 90 b = 44.8 β = 114.392 c = 62.132 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 PIXEL DECTRIS PILATUS 200K 2021-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.16 50 97.1 0.068 0.071 0.079 0.039 0.965 3.6 3.4 30307
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.32 84.4 0.133 0.116 0.114 0.965 20 2.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1DIC 2.166 35.189 9227 510 89.141 0.205 0.2018 0.2099 0.2629 0.2625 30.734
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] 0.081 0.019 -0.057 -0.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.299 r_dihedral_angle_6_deg 15.258 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_1_deg 7.995 r_lrange_it 7.582 r_lrange_other 7.577 r_scangle_it 4.186 r_scangle_other 4.184 r_mcangle_it 3.816 r_mcangle_other 3.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.299 r_dihedral_angle_6_deg 15.258 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_1_deg 7.995 r_lrange_it 7.582 r_lrange_other 7.577 r_scangle_it 4.186 r_scangle_other 4.184 r_mcangle_it 3.816 r_mcangle_other 3.814 r_scbond_it 2.811 r_scbond_other 2.809 r_mcbond_it 2.348 r_mcbond_other 2.342 r_chiral_restr_other 2.169 r_angle_refined_deg 1.402 r_angle_other_deg 0.701 r_symmetry_xyhbond_nbd_refined 0.267 r_nbd_refined 0.211 r_symmetry_nbd_refined 0.207 r_nbd_other 0.203 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.057 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing