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Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3350 15%, thiocyanate 0.4 M and ammonium iodide 0.1 M
Crystal Properties Matthews coefficient Solvent content 2.4 48.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.23 α = 90 b = 79.53 β = 100.78 c = 79.74 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2013-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.43 79.53 98.8 0.075 10.5 3.3 35498
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.49 96.9 0.56 1.9 3
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 (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 5M7M 2.43 75.87 33705 1778 98.77 0.20866 0.20671 0.2103 0.24473 0.2483 RANDOM 41.347
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] -0.05 -0.07 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.62 r_dihedral_angle_4_deg 13.922 r_dihedral_angle_3_deg 12.009 r_dihedral_angle_1_deg 6.151 r_long_range_B_refined 4.331 r_long_range_B_other 4.331 r_scangle_other 2.449 r_mcangle_it 2.423 r_mcangle_other 2.423 r_scbond_it 1.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.62 r_dihedral_angle_4_deg 13.922 r_dihedral_angle_3_deg 12.009 r_dihedral_angle_1_deg 6.151 r_long_range_B_refined 4.331 r_long_range_B_other 4.331 r_scangle_other 2.449 r_mcangle_it 2.423 r_mcangle_other 2.423 r_scbond_it 1.547 r_scbond_other 1.547 r_mcbond_it 1.43 r_mcbond_other 1.429 r_angle_refined_deg 1.216 r_angle_other_deg 0.906 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6062 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing