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Discovery of a Small Molecule ITK and Pan-TRK Kinase Inhibitor (PF-07245303) for the Potential Topical Treatment of Atopic Dermatitis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PQN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 12% PEG 3350, 0.1 M magnesium acetate and 0.1 M HEPES, pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.23 α = 90 b = 68.67 β = 106.94 c = 49.51 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 PILATUS 6M 2019-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.348 38.38 87.9 0.08 0.096 0.052 0.996 8.7 3.2 38323
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 1.355 1.46 0.881 1.07 0.598 0.393
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 1.348 26.34 38323 1884 67.5 0.1844 0.1822 0.1825 0.2274 0.2186 RANDOM 19.73
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] -0.8979 -0.112 0.3841 0.5138
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.68 t_omega_torsion 4.03 t_angle_deg 1.12 t_bond_d 0.012 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2115 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 33
Software Software Software Name Purpose BUSTER refinement XDS data reduction autoPROC data scaling PHASER phasing