SMTL ID : 9n6p.1

Room Temperature X-Ray Structure of SARS-CoV-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Ensitrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 7YY: 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione(Non-covalent)

7YY.1: 18 residues within 4Å: Chain A: T.24, T.25, T.26, L.27, H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.186, R.187, Q.188 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.25 Hydrogen bonds: A:T.26, A:G.143, A:S.144, A:S.144, A:C.145, A:E.166 Water bridges: A:N.142, A:N.142, A:N.142 pi-Stacking: A:H.41 Halogen bonds: A:Q.188 7YY.3: 18 residues within 4Å: Chain B: T.24, T.25, T.26, L.27, H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.186, R.187, Q.188 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.25 Hydrogen bonds: B:T.26, B:G.143, B:S.144, B:S.144, B:C.145, B:E.166, B:E.166 Water bridges: B:N.142, B:N.142, B:N.142 pi-Stacking: B:H.41 Halogen bonds: B:Q.188

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: N.220, R.221, F.222, D.262, A.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:D.262 NA.4: 5 residues within 4Å: Chain B: N.220, R.221, F.222, D.262, A.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.220, B:S.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bhandari, D. et al., Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir. Commun Biol (2025)

Release Date

2025-07-30

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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