5TQ7

Design and Synthesis of a pan-JAK Kinase Inhibitor Clinical Candidate (PF-06263276) Suitable for Inhaled and Topical Delivery for the Treatment of Inflammatory Diseases of the Lungs and Skin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TJC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.1 M Hepes, pH 7.5, 100 mM sodium acetate, 30% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.061α = 90
b = 185.108β = 110.64
c = 52.492γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21ALS5.0.2

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
12.133.68710.213.9230766

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 REPLACEMENTTHROUGHOUT3tjc2.133.6827533146875.520.228910.22580.28575RANDOM25.78
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.58
r_dihedral_angle_4_deg20.882
r_dihedral_angle_3_deg18.005
r_long_range_B_refined6.445
r_long_range_B_other6.445
r_dihedral_angle_1_deg6.361
r_scangle_other4.338
r_mcangle_it3.313
r_mcangle_other3.313
r_scbond_it2.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.58
r_dihedral_angle_4_deg20.882
r_dihedral_angle_3_deg18.005
r_long_range_B_refined6.445
r_long_range_B_other6.445
r_dihedral_angle_1_deg6.361
r_scangle_other4.338
r_mcangle_it3.313
r_mcangle_other3.313
r_scbond_it2.981
r_scbond_other2.981
r_mcbond_it2.409
r_mcbond_other2.409
r_angle_refined_deg1.693
r_angle_other_deg1.083
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.002
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 Atoms4475
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing