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Discovery of (thienopyrimidin-2-yl)aminopyrimidines as Potent, Selective, and Orally Available Pan-PI3-Kinase and Dual Pan-PI3-Kinase/mTOR Inhibitors for the Treatment of Cancer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E8X PDB ENTRY 1E8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 PEG 3350, 0.2M NH4SO4, 0.1M Tris-HCl 8.5, vapor diffusion, hanging drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.095 α = 90 b = 67.727 β = 96.07 c = 107.455 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 CCD ADSC QUANTUM 315 2006-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 3 50 97.8 0.074 12.8 3.5 20541
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 3 3.11 83.1 0.362 2.7 1740
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 PDB ENTRY 1E8X 3 45.18 20480 1042 97.96 0.218 0.216 0.2238 0.271 0.2203 RANDOM 101.362
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] -0.02 1.84 2.01 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.488 r_dihedral_angle_3_deg 18.689 r_dihedral_angle_4_deg 18.515 r_dihedral_angle_1_deg 6.63 r_scangle_it 1.357 r_angle_refined_deg 1.316 r_angle_other_deg 0.885 r_scbond_it 0.879 r_mcangle_it 0.65 r_mcbond_it 0.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.488 r_dihedral_angle_3_deg 18.689 r_dihedral_angle_4_deg 18.515 r_dihedral_angle_1_deg 6.63 r_scangle_it 1.357 r_angle_refined_deg 1.316 r_angle_other_deg 0.885 r_scbond_it 0.879 r_mcangle_it 0.65 r_mcbond_it 0.552 r_nbd_refined 0.241 r_nbd_other 0.198 r_xyhbond_nbd_other 0.191 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.143 r_symmetry_vdw_other 0.116 r_nbtor_other 0.088 r_chiral_restr 0.07 r_mcbond_other 0.064 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6820 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction