3OW4

Discovery of dihydrothieno- and dihydrofuropyrimidines as potent pan Akt inhibitors


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Under oil7.52938.3 mg/ml AKT1 protein, preincubated with 0.6 mM GSK3B peptide, 5 mM Mn-AMP-PNP. The precipitant was 20% PEG 4K, 15% isopropanol, 100 mM Hepes, pH 7.5, Under oil, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6353.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.427α = 90
b = 55.823β = 103.93
c = 91.354γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic confocal2005-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.63086.70.0510.04316.93.52616122796
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.7450.30.1070.0848.62.73727

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.627.4722769111086.30.196890.193290.26756RANDOM47.824
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]
0.811.110.06-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.403
r_dihedral_angle_4_deg20.625
r_dihedral_angle_3_deg19.501
r_dihedral_angle_1_deg6.719
r_scangle_it3.338
r_scbond_it1.991
r_angle_refined_deg1.665
r_mcangle_it1.376
r_mcbond_it0.706
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.403
r_dihedral_angle_4_deg20.625
r_dihedral_angle_3_deg19.501
r_dihedral_angle_1_deg6.719
r_scangle_it3.338
r_scbond_it1.991
r_angle_refined_deg1.665
r_mcangle_it1.376
r_mcbond_it0.706
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.006
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5366
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms60

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling