Table 2 Molecular docking of various proteins of coronavirus with quercetin ligand
From: Perspectives on plant flavonoid quercetin-based drugs for novel SARS-CoV-2
Sl. no. | Protein | PDB ID and chain | Best binding energy (kcal/Mol) | Interacting residues having H bond | Protein structure at PDB | Remarks |
|---|---|---|---|---|---|---|
1 | 2019-nCoV main protease (3CLpro) | 6LU7.A, 6Y84.A, 6YB7.A | − 6.71 | LYS88, TYR101, LYS137, GLY138, ASP289, GLY143, CYS145 |
| Non-structural polyprotein 1ab. Key enzyme mediating viral replication and transcription [64]. The active site residues from individual PDB structures were separately predicted using CASTp, each structure was docked separately, and interacting residues were identified. |
2 | 2019-nCoV RBD of spike glycoprotein/ human ACE2-BOAT1 complex | 6M17.E | − 5.56 | SER349, LEU441, ASN450 |
| Angiotensin-converting enzyme 2 (ACE2) is the human cellular receptor for SARS coronavirus (SARS-CoV) by interaction with the receptor-binding domain (RBD) of the surface Spike glycoprotein (S protein) of SARS-CoV-2 [65] |
3 | 2019-nCoV spike glycoprotein | 6VXX.A | − 5.19 | ASP88, ASP198, ILE233, ILE235 |
| Homotrimer protein [66] |
4 | 2019-nCoV RNA replicase | 6W9Q.A | − 5.89 | LEU45, THR109 |
| Non-structural protein 9 |
5 | 2019-nCoV RNA binding protein | 6W4B.A | − 5.44 | PRO58, THR68 |
| Non-structural protein 9 |
6 | 2019-nCoV papain-like protease | 6W9C.A | − 4.18 | GLN30 |
| Hydrolase enzyme, Homo 3-mer - A3 |
7 | SARS coronavirus papain-like protease/ deubiquitinase | 3E9S.A | − 3.37 | LYS158, ASP165, THR169 |
| Replication of SARS coronavirus requires proteolytic processing of the replicase polyprotein by two cysteine proteases, a chymotrypsin-like protease (3CLpro) and a papain-like protease (PLpro) [67, 68] |
8 | 2019-nCoV RNA-dependent RNA polymerase | 7BTF.A, 6M71.A, 6NUR.A | − 5.41 | TYR619, CYS622, ASP623, ASP761, SER841 |
| Non-structural protein 12, catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of COVID-19 virus [69]. The active site residues from individual PDB structures were separately predicted using CASTp; each structure was docked separately and interacting residues were identified. |
9 | SARS coronavirus main peptidase | 2A5I.A | − 5.12 | TYR54, GLU55, ASP187 |
| |
10 | SARS coronavirus main peptidase with an additional Ala at the N-terminus of each protomer | 2GTB.A | − 5.20 | THR111, ASP153 |
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