Computational protocol: Crystal Structures of Three Classes of Non-Steroidal Anti-Inflammatory Drugs in Complex with Aldo-Keto Reductase 1C3

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Protocol publication

[…] Data were processed using XDS and scaled with SCALA , and structures determined by molecular replacement using PHASER with the AKR1C3/NADP+ structure PDB ID 1S1P as the search model. Models were completed with several cycles of manual building with Coot and refinement with REFMAC . The active site electron density was closely inspected and the appropriate NSAID molecules, built using the Dundee PRODRG2 server , were fitted and refined by real space refinement. Solvent molecules were added by automatic peak picking from an Fo-Fc electron density map using Coot. Peaks above 3σ were selected and water molecules were manually checked in Coot. The final structures were refined with REFMAC TLS (translation libration screw) paired with maximum-likelihood restrained refinement. Stereochemistry of the final structures was evaluated using the Molprobity server . Final refinement statistics are given in . […]

Pipeline specifications

Software tools XDS, CCP4, Coot, PRODRG, MolProbity
Applications Drug design, Small-angle scattering, Protein structure analysis
Diseases Breast Neoplasms, Neoplasms
Chemicals Flufenamic Acid, Flurbiprofen, Ibuprofen, Indomethacin, Meclofenamic Acid, Mefenamic Acid, NADP, Naproxen, Sulindac