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VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context- dependent cytostasis in cancer cells
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other APO PDK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.8 pH 5.8
Crystal Properties Matthews coefficient Solvent content 3.12 60.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.838 α = 90 b = 108.838 β = 90 c = 84.401 γ = 120
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 RAXIS4 OSMIC BLUE 2011-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.5 30 99.1 0.1 13.8 3 19916 2
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 2.5 2.61 99.1 0.58 2.55 1.5
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 APO PDK2 2.49 29.46 18674 1002 98.72 0.18267 0.17973 0.1806 0.23729 0.2381 RANDOM 36.549
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] 0.35 0.35 0.35 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.321 r_dihedral_angle_4_deg 20.239 r_dihedral_angle_3_deg 18.686 r_dihedral_angle_1_deg 6.95 r_angle_refined_deg 2.073 r_chiral_restr 0.133 r_bond_refined_d 0.017 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 34.321 r_dihedral_angle_4_deg 20.239 r_dihedral_angle_3_deg 18.686 r_dihedral_angle_1_deg 6.95 r_angle_refined_deg 2.073 r_chiral_restr 0.133 r_bond_refined_d 0.017 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 2753 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing