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Targeting conserved water molecules: Design of 4-aryl-5-cyanopyrrolo[2,3-d]pyrimidine Hsp90 inhibitors using fragment-based screening and structure-based optimization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UY6 PDB ENTRY 1UY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 25% PEG MME 2000, 0.1M Na Cacodylate, PH6.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.659 α = 90 b = 89.764 β = 90 c = 98.251 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Osmic Blue Mirrors 2011-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5412
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.698 66.271 85.2 69745 27212 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.698 1.74 32.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 1UY6 1.698 66.27 2 2 69745 25703 1383 84.78 0.18718 0.18415 0.1846 0.24276 0.2416 RANDOM 29.473
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] 0.94 -0.58 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.313 r_dihedral_angle_4_deg 22.389 r_dihedral_angle_3_deg 15.071 r_dihedral_angle_1_deg 7.111 r_angle_refined_deg 2.217 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.313 r_dihedral_angle_4_deg 22.389 r_dihedral_angle_3_deg 15.071 r_dihedral_angle_1_deg 7.111 r_angle_refined_deg 2.217 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 1622 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 29
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling