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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 5.8 293 peg4k 25% , 0.1M MES 5.8 buffer
Crystal Properties Matthews coefficient Solvent content 2.13 42.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.898 α = 90 b = 73.032 β = 90 c = 240.864 γ = 90
Symmetry Space Group P 2 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 170 PIXEL DECTRIS PILATUS 200K 2021-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 74.5 0.15 0.311 0.771 5.4 3.2 36438
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 46.1 0.771 1.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1dic 2.214 46.46 34591 1694 85.164 0.229 0.225 0.2998 0.2828 33.495
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] -0.048 0.06 -0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.685 r_dihedral_angle_3_deg 16.172 r_dihedral_angle_6_deg 14.435 r_dihedral_angle_1_deg 7.637 r_lrange_it 7.311 r_lrange_other 7.307 r_mcangle_other 4.261 r_mcangle_it 4.26 r_scangle_it 4.219 r_scangle_other 4.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.685 r_dihedral_angle_3_deg 16.172 r_dihedral_angle_6_deg 14.435 r_dihedral_angle_1_deg 7.637 r_lrange_it 7.311 r_lrange_other 7.307 r_mcangle_other 4.261 r_mcangle_it 4.26 r_scangle_it 4.219 r_scangle_other 4.219 r_mcbond_it 2.762 r_mcbond_other 2.762 r_scbond_it 2.756 r_scbond_other 2.756 r_angle_refined_deg 1.372 r_chiral_restr_other 1.007 r_angle_other_deg 0.533 r_symmetry_xyhbond_nbd_refined 0.343 r_symmetry_nbd_refined 0.229 r_nbd_other 0.229 r_nbd_refined 0.217 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.056 r_bond_refined_d 0.007 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 6484 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing