SMTL ID : 7u29.1

Structure of SARS-CoV-2 Mpro mutant (K90R) in complex with Nirmatrelvir (PF-07321332)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 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: 20 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, E.166, L.167, H.172, D.187, R.188, Q.189, T.190, Q.192 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.41, A:M.165, A:E.166 Hydrogen bonds: A:F.140, A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:T.190 pi-Stacking: A:H.41 Halogen bonds: A:Q.192 Water bridges: B:S.1 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, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.41, B:E.166 Hydrogen bonds: B:F.140, B:G.143, B:C.145, B:H.164, B:E.166, B:E.166, B:T.190 Halogen bonds: B:T.190, B:Q.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Greasley, S.E. et al., Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. J.Biol.Chem. (2022)

Release Date

2022-03-09

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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