Almost everyone is susceptible to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an RNA virus, which can cause many symptoms and even death among high-risk individuals [1,2].The main protease (Mpro, also known as 3CLpro) is a cysteine protease essential for producing infectious virions and thus,an attractive target for drug development.Up to now, many studies using either in silico ligand docking or drug discovery based on available structures have been performed to discover new Mpro-inhibiting agents [3,4].However, most studies have used either peptidomimetics or covalent inhibitors for Mpro, which may introduce non-specific reactions with host proteins.Here, we presented the structure of shikonin in a non-covalent binding configuration with Mpro and compared it with covalent bonding structures in pursuit of novel scaffolds capable of inhibiting the main protease.rnAs shown in Fig.1, the crystal structure of Mpro in complex with shikonin (ShiMpro) is resolved at 2.45 (A) (Fig.1a and Table S1 online),and shikonin binds to only one of the protomers (i.e., protomer A) despite their overall structural similarity (Fig.S1 online, Supplementary materials and methods online).ShiMpro shows the same overall fold as for the apo structure of Mpro at pH 7.5 (apoMpro)[5].The root mean square (RMS) difference of equivalent Cα positions between apo and ShiMpro is ～ 0.3 (A) (Fig.1b).