5OQ4 | pdb_00005oq4

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E8Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	290.15	16% PEG 4000, 250mM (NH4)2SO4 and 100mM Tris pH7.5

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

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

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r	Bent cylindrical mirrors	2009-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.00715	ESRF	ID23-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.7	61	97	0.062	0.04	0.998	12.6	3.4		24608			50.65

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)	Redundancy	Number Unique Reflections (All)
1	2.7	2.85	92.9		0.49	0.308	0.809	2.4	3.3

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	1E8Y	2.7	61	24405	1292	96.95	0.19981	0.19643	0.2	0.26422	0.26	RANDOM	64.057

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]
-4.58		0.61	1.3		3.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.079
r_dihedral_angle_4_deg	19.47
r_dihedral_angle_3_deg	18.074
r_long_range_B_refined	9.671
r_long_range_B_other	9.671
r_dihedral_angle_1_deg	7.511
r_mcangle_it	4.954
r_mcangle_other	4.954
r_scangle_other	4.94
r_scbond_it	3.043
r_scbond_other	3.018
r_mcbond_it	3.003
r_mcbond_other	3.002
r_angle_refined_deg	1.98
r_angle_other_deg	1.255
r_chiral_restr	0.112
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.003
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 Atoms	Number
Protein Atoms	6769
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing