5OQ4

PQR309 - a Potent, Brain-Penetrant, Orally Bioavailable, pan-Class I PI3K/mTOR Inhibitor as Clinical Candidate in Oncology


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E8Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5290.1516% PEG 4000, 250mM (NH4)2SO4 and 100mM Tris pH7.5
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.49α = 90
b = 67.36β = 96.94
c = 103.61γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rBent cylindrical mirrors2009-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.00715ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.761970.0620.040.99812.63.42460850.65
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8592.90.490.3080.8092.43.3

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 REPLACEMENTTHROUGHOUT1E8Y2.76124405129296.950.199810.196430.26422RANDOM64.057
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]
-4.580.611.33.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.079
r_dihedral_angle_4_deg19.47
r_dihedral_angle_3_deg18.074
r_long_range_B_refined9.671
r_long_range_B_other9.671
r_dihedral_angle_1_deg7.511
r_mcangle_it4.954
r_mcangle_other4.954
r_scangle_other4.94
r_scbond_it3.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.079
r_dihedral_angle_4_deg19.47
r_dihedral_angle_3_deg18.074
r_long_range_B_refined9.671
r_long_range_B_other9.671
r_dihedral_angle_1_deg7.511
r_mcangle_it4.954
r_mcangle_other4.954
r_scangle_other4.94
r_scbond_it3.043
r_scbond_other3.018
r_mcbond_it3.003
r_mcbond_other3.002
r_angle_refined_deg1.98
r_angle_other_deg1.255
r_chiral_restr0.112
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6769
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing