SMTL ID : 8cae.1

Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 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: 18 residues within 4Å: Chain A: H.41, M.49, F.140, L.141, N.142, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, Y.172, R.188, Q.189, T.190, Q.192 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.41, A:M.49, A:M.165, A:E.166 Hydrogen bonds: A:H.41, A:F.140, A:L.141, A:G.143, A:S.144, A:C.145, A:E.166, A:E.166, A:E.166, A:T.190 Halogen bonds: A:Q.192 4WI.2: 18 residues within 4Å: Chain B: H.41, M.49, F.140, L.141, N.142, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, Y.172, R.188, Q.189, T.190, Q.192 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:H.41, B:M.49, B:M.165, B:E.166 Hydrogen bonds: B:H.41, B:F.140, B:L.141, B:G.143, B:S.144, B:C.145, B:E.166, B:E.166, B:T.190 Halogen bonds: B:Q.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El Kilani, H. et al., 13b-K and Nirmatrelvir Resistance Mutations of SARS-CoV-2 Main Protease: Structural, Biochemical, and Biophysical Characterization of Free Enzymes and Inhibitor Complexes. Crystals (2025)

Release Date

2025-08-06

Peptides

Non-structural protein 11: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Non-structural protein 11