SMTL ID : 8h3g.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 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: 19 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 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.6: 19 residues within 4Å: Chain A: S.1 Chain B: 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, 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.8, P.9, I.152, Y.154 Chain B: P.122, S.123 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.154 Water bridges: A:K.12, A:D.153, B:P.122 GOL.3: 9 residues within 4Å: Chain A: M.6, A.7, F.8, S.113, Q.127, R.298 Chain B: S.123, G.124 Ligands: GOL.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.113, A:Q.127, B:S.123 Water bridges: A:D.295 GOL.4: 3 residues within 4Å: Chain A: N.84, E.178, N.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.84, A:E.178, A:N.180, A:N.180 GOL.5: 7 residues within 4Å: Chain A: M.6, R.298, Q.299 Chain B: Y.118, S.123, L.141 Ligands: GOL.3 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.118, B:S.123, A:R.298 Water bridges: B:S.139

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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