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4-Arylazo-3,5-diamino-1H-pyrazole CDK Inhibitors: SAR Study, Crystal Structure in Complex with CDK2, Selectivity, and Cellular Effects
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C5Y PDB ENTRY 2C5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 277 10% PEG 3350, NAF, PH 7.0, VAPOUR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Crystal Properties Matthews coefficient Solvent content 1.84 32.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.37 α = 90 b = 70.75 β = 90 c = 72.18 γ = 90
Symmetry Space Group P 21 21 21
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 MIRRORS 2004-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D
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 1.8 29.9 99.3 0.04 16.9 3.43 25793 2.8
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 1.8 1.86 97.5 0.37 2.8 2.67
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2C5Y 1.8 29 24966 826 99.3 0.18 0.178 0.231 0.23 RANDOM 36.23
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] 0.45 0.44 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.006 r_dihedral_angle_4_deg 24.552 r_dihedral_angle_3_deg 21.775 r_scangle_it 8.388 r_dihedral_angle_1_deg 8.342 r_scbond_it 6.469 r_mcangle_it 4.256 r_mcbond_it 3.613 r_angle_refined_deg 1.994 r_angle_other_deg 1.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.006 r_dihedral_angle_4_deg 24.552 r_dihedral_angle_3_deg 21.775 r_scangle_it 8.388 r_dihedral_angle_1_deg 8.342 r_scbond_it 6.469 r_mcangle_it 4.256 r_mcbond_it 3.613 r_angle_refined_deg 1.994 r_angle_other_deg 1.266 r_nbd_refined 0.295 r_symmetry_hbond_refined 0.294 r_xyhbond_nbd_refined 0.293 r_symmetry_vdw_other 0.284 r_symmetry_vdw_refined 0.267 r_nbd_other 0.256 r_nbtor_refined 0.197 r_chiral_restr 0.136 r_nbtor_other 0.102 r_gen_planes_refined 0.015 r_bond_refined_d 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2357 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing