SMTL ID : 9cjr.1

X-ray crystal structure of SARS-CoV-2 main protease double mutants in complex with Ensitrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: 20 residues within 4Å: Chain A: T.24, T.25, T.26, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, H.172, D.187, R.188, Q.189 Chain B: S.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.25, A:M.165 Hydrogen bonds: A:T.26, A:G.143, A:S.144, A:S.144, A:C.145, A:V.166 Water bridges: A:Q.189 pi-Stacking: A:H.41 7YY.4: 20 residues within 4Å: Chain B: T.24, T.25, T.26, L.27, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, H.172, D.187, R.188, Q.189 8 PLIP interactions: 8 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:V.166 pi-Stacking: B:H.41

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: N.221, F.223, D.263, A.266, S.267 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.221, A:F.223, A:D.263, A:D.263, H2O.1 MG.5: 5 residues within 4Å: Chain B: N.221, F.223, D.263, A.266, S.267 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.221, B:F.223, B:D.263, B:D.263, H2O.6

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: T.226, L.227 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: R.188, T.190 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esler, M.A. et al., X-ray crystal structure of SARS-CoV-2 main protease double mutants in complex with Ensitrelvir. To Be Published

Release Date

2025-07-09

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5