SMTL ID : 8h51.1

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x 4WI: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide(Covalent)

4WI.1: 22 residues within 4Å: Chain A: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 Chain B: S.1 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.41, A:V.166 Hydrogen bonds: A:G.143, A:C.145, A:H.164, A:V.166, A:V.166, A:T.190, B:S.1, B:S.1 Halogen bonds: A:V.166, A:Q.192 Water bridges: B:S.1 4WI.2: 22 residues within 4Å: Chain A: S.1 Chain B: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.41, B:V.166 Hydrogen bonds: B:G.143, B:C.145, B:H.164, B:V.166, B:V.166, B:T.190, A:S.1, A:S.1 Halogen bonds: B:V.166, B:Q.192 Water bridges: A:S.1

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
A

3C-like proteinase nsp5