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Discovery of NVP-CGM097 - a highly potent and selective MDM2 inhibitor undergoing phase 1 clinical trials in p53wt tumors: Hdm2 (MDM2) complexed with NVP-CGM097
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 reservoir: 2M AmSulfate, 0.1M cictric acid, pH4.5, protein: 7mg/ml Hdm2 in 50mM TRIS pH8.0, 200mM NaCl, 1mM TCEP, 10% glycerol, drop: 1ul reservoir + 1ul protein
Crystal Properties Matthews coefficient Solvent content 2.17 43.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.609 α = 90 b = 55.609 β = 90 c = 108.28 γ = 120
Symmetry Space Group P 61 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 PIXEL PSI PILATUS 6M 2010-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00000 SLS X10SA
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 19.75 99.9 0.075 29.1 20.4 9762 -3
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 1.85 100 0.629 5.8 19.5
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 4ZYI 1.8 19.75 9273 488 100 0.227 0.2267 0.225 0.2321 0.2302 RANDOM 24.274
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] 0.26 0.13 0.26 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.963 r_dihedral_angle_4_deg 15.745 r_dihedral_angle_3_deg 14.13 r_dihedral_angle_1_deg 5.305 r_angle_refined_deg 1.04 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 765 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 48
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing APRV data reduction