SMTL ID : 9avq.1

Crystal structure of SARS-CoV-2 main protease A191T mutant in complex with an inhibitor Nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.41, 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:T.190 Halogen bonds: A:Q.192 4WI.3: 20 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, 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:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:T.190 Halogen bonds: B:Q.192

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: H.80, S.81, K.88, K.90 No protein-ligand interaction detected (PLIP) PEG.4: 4 residues within 4Å: Chain B: H.80, S.81, K.88, K.90 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hattori, S.I. et al., Structural and virologic mechanism of the emergence of resistance to M pro inhibitors in SARS-CoV-2. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-04-24

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5