SMTL ID : 8dcz.1

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) M165Y Mutant in Complex with Nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 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: 21 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, Y.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.41, A:Y.165, A:E.166 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:E.166 Halogen bonds: A:Y.165 4WI.2: 21 residues within 4Å: Chain B: H.41, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, Y.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, A.191 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.41, B:Y.165, B:E.166 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, A:S.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Y. et al., Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir. Biorxiv (2022)

Release Date

2022-07-13

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5