This page contains covalent docking libraries of commercially available compounds developed for two papers:
Mpro paper
Elissa A. Fink, Conner Bardine, Stefan Gahbauer, Isha Singh, Kris White, Shuo Gu,
Xiaobo Wan, Beatrice Ary, Isabella Glenn, Joseph O'Connell, Henry O'Donnell,
Pavla Fajtova, Jiankun Lyu, Seth Vigneron, Nicholas J. Young, Ivan S. Kondratov,
Anthony J. O'Donoghue, Yurii Moroz, Jack Taunton, Adam R. Renslo, John J. Irwin,
Adolfo García-Sastre, Brian K. Shoichet, Charles S Craik,
Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors,
bioRxiv 2022.07.05.498881; doi: https://doi.org/10.1101/2022.07.05.498881
Nsp14 paper
Isha Singh, Fengling Li, Elissa Fink, Irene Chau, Alice Li, Annia Rodriguez-Hernandez
Isabella Glenn, Francisco J. Zapatero-Belinchón, Mario Rodriguez, Kanchan Devkot,
Zhijie Deng, Kris White, Xiaobo Wan, Nataliya A. Tolmachova, Yurii S. Moroz, H.
Umit Kaniskan, Melanie Ott, Adolfo Gastía-Sastre, Jian Jin, Danica Galoic Fujimori,
John J. Irwin, Masoud Vedadi, Brian K. Shoichet,
Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7-methyltransferase
bioRxiv 2023.01.12.523677; doi: https://doi.org/10.1101/2023.01.12.523677
The databases below are free to download. If you use them, please cite the relevant paper.
These libraries are free to use, but you must use them at your own risk.
Nitriles for Mpro
In 2D:
(smiles pending)
In 3D:
lead-like:
wget http://covalent2022.docking.org/get_nitrile2_leads_3d.cmd
bash get_nitrile2_leads_3d.cmd
frag-like:
wget http://covalent2022.docking.org/get_nitrile2_fragments_3d.cmd
bash get_nitrile2_fragments_3d.cmd
Acrylamides for Nsp14
In 2D: (17,526,957 molecules)
wget http://covalent2022.docking.org/acrylamides.smi.gz
In 3D: (17,713 db2.gz files total)
wget http://covalent2022.docking.org/get_acrylamides_3d.cmd
bash get_acrylamides_3d.cmd
Aldehydes for Mpro 2020
In 2D: (2,510,964 molecules)
wget http://covalent2022.docking.org/aldehydes_mpro_2020.smi.gz
In 3D: (2083 db2.gz fragment files and 28878 db2.gz leadlike files)
wget http://covalent2022.docking.org/get_aldehydes_2020_fragments_3d.cmd
bash get_aldehydes_2020_fragments_3d.cmd
wget http://covalent2022.docking.org/get_aldehydes_2020_leadlike_3d.cmd
bash get_aldehydes_2020_leadlike_3d.cmd
Ketoamides for Mpro
In 2D: (1,521,347 molecules)
wget http://covalent2022.docking.org/ketoamides.smi.gz
In 3D: (5819 db2.gz files)
wget http://covalent2022.docking.org/get_ketoamides_3d.cmd
bash get_ketoamides_3d.cmd
Aldehydes for Nsp14 2021
In 2D: (4,729,871 molecules)
wget http://covalent2022.docking.org/aldehydes_nsp14_2021.smi.gz
in 3D: (4728 db2.gz files)
wget http://covalent2022.docking.org/get_aldehydes_2021_3d.cmd
bash get_aldehydes_2021_fragments_3d.cmd
Last updated: Mar 17, 2023 by John Irwin