SMTL ID : 8e26.1

Crystal Structure of SARS-CoV-2 Main Protease N142S mutant in complex with Nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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: 24 residues within 4Å: Chain A: L.27, H.41, C.44, M.49, Y.54, F.140, L.141, S.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 Chain B: S.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.41, A:E.166, A:Q.189 Hydrogen bonds: A:G.143, A:C.145, A:H.163, A:H.164, A:E.166, A:E.166, A:E.166, A:Q.189 Halogen bonds: A:Q.192 4WI.2: 23 residues within 4Å: Chain A: S.1 Chain B: L.27, H.41, M.49, Y.54, F.140, L.141, S.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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165, B:E.166 Hydrogen bonds: B:F.140, B:G.143, B:S.144, B:C.145, B:H.163, B:H.164, B:E.166, B:E.166, B:H.172

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 11 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, P.9, Q.127, D.295, R.298, Q.299, F.305 2 PLIP interactions: 2 interactions with chain B Water bridges: B:M.6 pi-Cation interactions: B:F.8 DMS.4: 5 residues within 4Å: Chain B: R.40, P.52, N.53, Y.54, E.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noske, G.D. et al., Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease. J.Biol.Chem. (2023)

Release Date

2022-10-12

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5