SMTL ID : 8h3k.1

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Enstrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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, 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, D.187, R.188, Q.189 Ligands: VIB.2 9 PLIP interactions: 9 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 pi-Stacking: A:H.41 7YY.3: 19 residues within 4Å: Chain A: S.1 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, V.166, D.187, R.188, Q.189 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.25, B:M.165 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

1 x VIB: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM(Non-covalent)

VIB.2: 5 residues within 4Å: Chain A: S.46, E.47, M.49, Q.189 Ligands: 7YY.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.46

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: R.105, I.106, Q.107, P.108, F.134, Y.182 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.105, B:I.106, B:Q.107, B:Q.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, Y. et al., Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature (2023)

Release Date

2023-10-11

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5

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