SARS-CoV-2 Ligands Database

Last updated January 4, 2026

The molecular structure of SARS-CoV-2 S protein

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a phosphorylated nucleocapsid protein with a single-stranded genomic RNA as its core. The viral core is encapsulated by phospholipid bilayers to form spherical or pleomorphic particles of 80–120 nm in size and is characterized by the presence of the outer surface spike (S) protein.

The S protein is a highly glycosylated type I membrane protein anchored in the viral membrane. The S protein is composed of two subunits, S1 and S2. S1 is responsible for the recognition of the host cell surface receptor (ACE2), which allows viral entry; the S2 subunit is mainly responsible for subsequent viral fusion with and entry into the host cell.

The junction of S1 and S2 contains a specific furin cleavage site, which is cleaved by host cell furin, facilitating viral entry into cells. The S1 subunit contains the N-terminal domain (NTD), the receptor binding domain (RBD), and the C-terminal domains (CTD1 and CTD2). The S2 subunit contains the fusion peptide (FP), heptad repeat 1 (HR1), and heptad repeat 2 (HR2).

The proposed database allows searching for complexes of individual SAPS domains (Domains tab), with ligands (Ace and antibodies), as well as generating lists of SAPS complexes with different numbers of ligands (Ace and antibodies) - Ligands tab.

The proposed database contains all resolved S protein complexes (UniProt ID: P0DTC2), available in the PDB.