4JNM

Discovery of Potent and Efficacious Urea-containing Nicotinamide Phosphoribosyltransferase (NAMPT) Inhibitors with Reduced CYP2C9 Inhibition Properties


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 292.0
Details 0.2uL + 0.2uL drops containing 6mg/mL Nampt, 0.1M Sodium phosphate, 25-29% polyethylene glycol 3350, 0.2M NaCl, 1mM compound, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.44 α = 90
b = 106.32 β = 96.34
c = 82.82 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2012-10-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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
2.2 50 93.2 0.149 -- -- 3.3 52863 49268 2.0 1.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.2 2.28 62.2 -- 0.44 2.1 2.2 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.2 38.383 -- 1.33 53009 49223 2498 92.7 -- 0.2031 0.2006 0.2495 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2 2.2386 -- 96 1490 0.2533 0.2907 -- 53.0
X Ray Diffraction 2.2386 2.2843 -- 95 1827 0.2509 0.2788 -- 67.0
X Ray Diffraction 2.2843 2.334 -- 113 2088 0.2376 0.3578 -- 74.0
X Ray Diffraction 2.334 2.3883 -- 111 2358 0.2324 0.2726 -- 85.0
X Ray Diffraction 2.3883 2.448 -- 152 2629 0.2382 0.3062 -- 94.0
X Ray Diffraction 2.448 2.5142 -- 153 2775 0.2207 0.2937 -- 99.0
X Ray Diffraction 2.5142 2.5881 -- 149 2745 0.2216 0.2908 -- 99.0
X Ray Diffraction 2.5881 2.6717 -- 134 2791 0.2203 0.2671 -- 99.0
X Ray Diffraction 2.6717 2.7671 -- 149 2796 0.2315 0.3129 -- 99.0
X Ray Diffraction 2.7671 2.8779 -- 129 2799 0.2315 0.3078 -- 100.0
X Ray Diffraction 2.8779 3.0088 -- 152 2764 0.2336 0.2743 -- 100.0
X Ray Diffraction 3.0088 3.1674 -- 176 2775 0.2044 0.247 -- 100.0
X Ray Diffraction 3.1674 3.3657 -- 153 2802 0.2064 0.226 -- 100.0
X Ray Diffraction 3.3657 3.6254 -- 138 2801 0.1917 0.2504 -- 100.0
X Ray Diffraction 3.6254 3.9899 -- 151 2798 0.1806 0.2131 -- 100.0
X Ray Diffraction 3.9899 4.5664 -- 157 2795 0.1573 0.2076 -- 100.0
X Ray Diffraction 4.5664 5.7501 -- 141 2823 0.1707 0.1842 -- 100.0
X Ray Diffraction 5.7501 38.3889 -- 149 2869 0.1819 0.2445 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 17.4358
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.2746
Anisotropic B[2][2] 7.4055
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.1601
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_angle_d 0.695
f_plane_restr 0.003
f_dihedral_angle_d 11.17
f_chiral_restr 0.05
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7543
Nucleic Acid Atoms 0
Heterogen Atoms 114
Solvent Atoms 603

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.3_928)
HKL-2000 data reduction
HKL-2000 data scaling