4V25

VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context- dependent cytostasis in cancer cells


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherAPO PDK2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.80.1 M SODIUM ACETATE PH 5.8, 0.125 M MAGNESIUM CHLORIDE AND 6% ISOPROPANOL, 4OC
Crystal Properties
Matthews coefficientSolvent content
3.1260.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.944α = 90
b = 108.944β = 90
c = 84.38γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS4OSMIC BLUE2012-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.63098.30.1252.31172811.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6997.70.531.32.19

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAPO PDK22.625.011640387298.080.201320.198340.25619RANDOM63.207
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]
0.940.940.94-3.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.902
r_dihedral_angle_3_deg18.998
r_dihedral_angle_4_deg15.227
r_dihedral_angle_1_deg7.308
r_angle_refined_deg1.738
r_angle_other_deg0.885
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.902
r_dihedral_angle_3_deg18.998
r_dihedral_angle_4_deg15.227
r_dihedral_angle_1_deg7.308
r_angle_refined_deg1.738
r_angle_other_deg0.885
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2748
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing