Computational protocol: Discovery of a potent benzoxaborole-based anti-pneumococcal agent targeting leucyl-tRNA synthetase

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Protocol publication

[…] The structure of the apo form of SpLeuRS-CP1 was solved by molecular replacement implemented in the program MOLREP of the CCP4 suite using the structure of Aquifex aeolicus LeuRS CP1 (PDB entry: 3PZ5) as the starting search model. Initial structure refinement was carried out using the program REFINE in PHENIX according to the standard protocol. Final structure refinement was performed using the program REFMAC5. Model building was manually carried out using the program COOT. The structure of SpLeuRS-CP1 bound to ZCL039 was then determined by molecular replacement (MOLREP) using the structure of the apo form of SpLeuRS-CP1 as the starting model. Model building and refinement were carried out as described above. Structure refinement was performed using the program REFMAC5 and PHENIX. Throughout the refinement, 5% of randomly chosen reflections were set aside for free R-factor monitor. The quality of the final models was evaluated by PROCHECK. All the molecular graphics were generated using PyMOL (DeLano Scientific; http://www.pymol.org). […]

Pipeline specifications

Software tools Molrep, CCP4, PHENIX, REFMAC5, Coot, PROCHECK, PyMOL
Application Protein structure analysis
Organisms Streptococcus pneumoniae, Mycoplasma pneumoniae
Diseases Pneumonia, Bacterial