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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 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.635 α = 90 b = 67.391 β = 96.11 c = 106.674 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 2.7 40 98.1 0.044 20.7 3.2 27593
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 2.7 2.8 98.5 0.44 3.2 2717
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 2.9 20 22093 1125 98.11 0.241 0.238 0.3008 0.295 0.3369 RANDOM 71.16
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] 1.02 3.03 -0.59 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.637 r_dihedral_angle_3_deg 19.869 r_dihedral_angle_4_deg 19.221 r_dihedral_angle_1_deg 6.648 r_mcangle_it 4.48 r_scangle_it 3.186 r_mcbond_it 2.772 r_scbond_it 1.99 r_angle_refined_deg 1.278 r_angle_other_deg 0.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.637 r_dihedral_angle_3_deg 19.869 r_dihedral_angle_4_deg 19.221 r_dihedral_angle_1_deg 6.648 r_mcangle_it 4.48 r_scangle_it 3.186 r_mcbond_it 2.772 r_scbond_it 1.99 r_angle_refined_deg 1.278 r_angle_other_deg 0.784 r_mcbond_other 0.417 r_nbd_refined 0.23 r_symmetry_vdw_other 0.196 r_nbtor_refined 0.187 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.171 r_symmetry_vdw_refined 0.163 r_nbtor_other 0.085 r_chiral_restr 0.071 r_xyhbond_nbd_other 0.033 r_bond_refined_d 0.01 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 6812 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction