5MHP

Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M7M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 3350 15%, thiocyanate 0.4 M and ammonium iodide 0.1 M
Crystal Properties
Matthews coefficientSolvent content
2.448.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.23α = 90
b = 79.53β = 100.78
c = 79.74γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2013-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
12.4379.5398.80.07510.53.335498
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)
12.432.4996.90.561.93

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 REPLACEMENTTHROUGHOUT5M7M2.4375.8733705177898.770.208660.206710.24473RANDOM41.347
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]
-0.05-0.070.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.62
r_dihedral_angle_4_deg13.922
r_dihedral_angle_3_deg12.009
r_dihedral_angle_1_deg6.151
r_long_range_B_refined4.331
r_long_range_B_other4.331
r_scangle_other2.449
r_mcangle_it2.423
r_mcangle_other2.423
r_scbond_it1.547
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.62
r_dihedral_angle_4_deg13.922
r_dihedral_angle_3_deg12.009
r_dihedral_angle_1_deg6.151
r_long_range_B_refined4.331
r_long_range_B_other4.331
r_scangle_other2.449
r_mcangle_it2.423
r_mcangle_other2.423
r_scbond_it1.547
r_scbond_other1.547
r_mcbond_it1.43
r_mcbond_other1.429
r_angle_refined_deg1.216
r_angle_other_deg0.906
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6062
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing