Computational protocol: Small-molecule inhibition of TLR8 through stabilization of itsresting state

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Protocol publication

[…] Diffraction dataset was collected on beamline PF-AR NE3A (Ibaraki, Japan), PF BL-5A (Ibaraki, Japan), and SPring-8 BL41XU (Hyogo, Japan) under cryogenic condition at 100 K. The wavelength was set to 1.0000 Å. The dataset was processed using the HKL2000 package or iMOSFM. hTLR8/CU-CPT structures were determined by the molecular replacement method using the Molrep program with the unliganded hTLR8 structure (PDB ID: 3W3G) as a search model. The model was further refined with stepwise cycles of manual model building using the COOT program and restrained refinement using REFMAC until the R factor was converged. CU-CPT compounds, N-glycans, and water molecules were modeled into the electron density maps at the latter cycles of the refinement. The quality of the final structure was validated with the PDB validation server ( The favored and the allowed regions in the Ramachandran plot were 94 % and 6 % for TLR8/CU-CPT8m, and 94 % and 5 % for TLR8/CU-CPT9b. The statistics of the data collection and refinement are summarized in . The figures representing structures were prepared with PyMOL ( or CueMol ( Coordinates and structure factor have been deposited in the Protein Data Bank with PDB ID 5WYX (TLR8/CU-CPT8m), and 5WYZ (TLR8/CU-CPT9b). […]

Pipeline specifications

Software tools Molrep, Coot, PyMOL, CueMol
Databases wwPDB
Application Protein structure analysis
Organisms Bacteria, Homo sapiens