SMTL ID : 8dz6.1

Crystal Structure of SARS-CoV-2 Main protease mutant Q189K in complex with Nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 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: 22 residues within 4Å: Chain A: L.27, H.41, M.49, 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, K.189, T.190, Q.192 Chain B: S.1 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:S.1, A:F.140, A:G.143, A:S.144, A:S.144, A:C.145, A:H.163, A:H.164, A:E.166, A:E.166 Hydrophobic interactions: A:H.41, A:M.165 Halogen bonds: A:T.190 4WI.4: 23 residues within 4Å: Chain A: S.1 Chain B: L.27, 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, K.189, T.190, Q.192 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.41, B:M.165 Hydrogen bonds: B:G.143, B:S.144, B:S.144, B:C.145, B:H.163, B:H.164, B:E.166, B:E.166, B:E.166, B:H.172

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

DMS.2: 10 residues within 4Å: Chain A: E.14, G.15, C.16, M.17, V.18, W.31, A.70, G.71, N.95, G.120 No protein-ligand interaction detected (PLIP) DMS.3: 8 residues within 4Å: Chain A: M.6, A.7, F.8, T.111, S.113, Q.127, D.295, R.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.298 pi-Cation interactions: A:F.8 DMS.5: 9 residues within 4Å: Chain A: S.123, G.124 Chain B: M.6, A.7, F.8, Q.127, D.295, R.298, Q.299 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.127 Salt bridges: B:D.295 pi-Cation interactions: B:F.8

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

2022-10-05

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5