Journal of Medicinal Chemistry
Article
24% PEG3350, 0.2 M MgSO4, using a sitting drop format and
equilibrated against a reservoir of the crystallization solution. The
crystal was flash frozen with liquid nitrogen after being stabilized in a
cryobuffer containing 0.1 mM Tris pH 8.23, 24% PEG3350, 0.2 M
MgSO4, 20% ethylene glycol.
ACKNOWLEDGMENTS
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The authors thank all of the contributors to the EFT project
team.
X-ray Data Collection. Initial data from a single crystal of the EF-
Tu·compound 2 complex were collected on a ADSC Quantum 210
CCD detector using synchrotron radiation (λ = 1 Å) at the IMCA-
CAT beamline 17-ID of the Argonne Photon Source. Data were
collected using φ rotations of 0.5° and 180° of total data collected.
X-ray Data Processing, Structure Determination, and
Refinement. Data from the EF-Tu·compound 2 complex were
processed using the HKL2000 Suite, version 0.95.9 Data processing
statistics are shown in Table 2. Crystals were diffracted to 2.3 Å
ABBREVIATIONS USED
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MIC, minimum inhibitory concentration; EC50, 50% effective
dose; G+, Gram positive; MRSA, methicillin-resistant Staph-
ylococcus aureus; VRE, vancomycin-resistant enterococci; S.
aureus, Staphylococcus aureus; E. faecalis, Enterococcus faecalis; E.
faecium, Enterococcus faecium; S. pyogenes, Streptococcus pyogenes;
EF-Tu, elongation factor-Tu
REFERENCES
Table 2
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(1) Morris, R. P.; Leeds, J. A.; Naegeli, H. U.; Oberer, L.; Memmert,
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701. The structure was later corrected and verified: Tavecchia, P.;
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Restelli, E.; Ciabatti, R. Tetrahedron 1995, 51 (16), 4867−4890 . For
acidic decomposition, see above.
(3) (a) LaMarche, M. J.; Leeds, J. A.; Dzink-Fox, J.; Gunderson, K.;
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compound 2
data collection parameters (highest resolution shell)
resolution range (Å)
total observations
unique reflections
completeness (%)
I/σ
50−2.3 (2.38−2.3)
148 584
21 195
99.7 (100)
44.8 (8.0)
0.073
Rsym
refinement parameters
work/Rfree
R
0.212/0.258
3047
protein atoms
heterogen atoms (Mg/GDP/compd)
solvent atoms
87
117
average B-factor (Å2)
rms Deviations from ideal value
bond lengths (Å)
43.6
0.009
1.6
bond angles (deg)
resolution in the space group P2(1)2(1)2 with a unit cell of a = 80.305
Å, b = 123.577 Å, c = 45.092 Å, α = β = γ = 90°. Data collection
statistics are shown in Table 2. The structure of the EF-
Tu·GDP·compound 2 complex was determined by the molecular
replacement as implemented in PHASER,10 using E. coli EF-Tu
protein as a search model (1D8T). The resulting molecular
replacement solution contained one EF-Tu·GDP·compound 2 protein
complex in the asymmetric unit. Refinement was carried out with
CNX11 using a single round of rigid-body refinement, following several
cycles of simulated annealing refinement, B-factor refinement, and
model building with the COOT software package.12 Water molecules,
GDP, and the Mg2+ ion were added prior to addition of the ligand 2.
Refinement produced a final model with excellent geometry (rmsd
bond lengths 0.009 Å, rmsd bond angles 1.6°) and R-factors of Rwork
and Rfree of 21% and 26%, respectively.
(6) (a) Zubay, G. In Vitro Synthesis of Protein in Microbial Systems.
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Properties of CAP, the Catabolite Gene Activator. Methods Enzymol.
1980, 65, 856−877.
(7) Because of the lack of aqueous solubility, organic excipients were
necessary to enable formulation of 2 (5% DMA, 30% PEG400, 10%
cremophor EL, 5% 0.1 N NaOH, 50% pH 7.4 buffer).
ASSOCIATED CONTENT
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S
* Supporting Information
(8) Frimodt-Moller, N.; Knudesen, J. D.; Espersen, F. Handbook of
animal models of infection; Zak, O.; Sand, M. A., Eds.; Academic Press:
San Diego, 1999; pp 127−136. O’Reilly, T.; Cleeland, R.; Squires, E. L.
Antibiotics in laboratory medicine, 4th ed.;Lorian, V., Ed.; Williams &
Wilkins: Baltimore, 1996; pp 604−765.
(9) Otwinowski, Z.; Minor, W. Processing of X-ray Diffraction Data
Collected in Oscillation Mode. In Methods in Enzymology; Carter, C.
W., Jr.; Sweet, R. M., Eds.; Academic Press: New York, 1997; Vol. 276:
Macromolecular Crystallography, part A, pp 307−326.
(10) McCoy, A. J.; Grosse-Kunstleve, R. W.; Adams, P. D.; Winn, M.
D.; Storoni, L. C.; Read, R. J. Phaser crystallographic software. J. Appl.
Crystallogr. 2007, 40, 658−674.
Detailed synthetic procedures and compound characterization
data. This material is available free of charge via the Internet at
AUTHOR INFORMATION
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Corresponding Author
*Tel: (617) 871-7729. Fax: 617-871-4081. E-mail: matthew.
Notes
The authors declare no competing financial interest.
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dx.doi.org/10.1021/jm300783c | J. Med. Chem. 2012, 55, 6934−6941