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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 peg4k 20-30%
Crystal Properties Matthews coefficient Solvent content 2.08 40.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.507 α = 90 b = 44.955 β = 117.312 c = 63.417 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 150 PIXEL DECTRIS PILATUS 200K 2020-11-04 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) 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 1.98 50 98.3 0.085 0.087 0.044 0.916 14 3.7 12847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.05 87.9 0.2 0.16 0.916 3 2.1
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 (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 1.986 37.218 12811 662 98.199 0.2 0.1974 0.2068 0.2512 0.2603 25.135
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] 0.027 -0.02 0.06 -0.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.386 r_dihedral_angle_6_deg 16.359 r_dihedral_angle_3_deg 15.77 r_dihedral_angle_1_deg 7.97 r_lrange_it 6.44 r_lrange_other 6.418 r_scangle_it 4.412 r_scangle_other 4.41 r_scbond_it 2.895 r_scbond_other 2.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.386 r_dihedral_angle_6_deg 16.359 r_dihedral_angle_3_deg 15.77 r_dihedral_angle_1_deg 7.97 r_lrange_it 6.44 r_lrange_other 6.418 r_scangle_it 4.412 r_scangle_other 4.41 r_scbond_it 2.895 r_scbond_other 2.894 r_mcangle_it 2.794 r_mcangle_other 2.794 r_mcbond_it 1.962 r_mcbond_other 1.96 r_angle_refined_deg 1.428 r_angle_other_deg 0.485 r_nbd_refined 0.218 r_nbd_other 0.212 r_symmetry_nbd_other 0.2 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.164 r_symmetry_nbd_refined 0.152 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1595 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing