SMTL ID : 8b2t.1

SARS-CoV-2 Main Protease (Mpro) in complex with nirmatrelvir alkyne

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x OW1: Nirmatrelvir (reacted form)(Covalent)

OW1.1: 20 residues within 4Å: Chain A: H.41, M.49, Y.54, F.140, 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.41, A:E.166 Hydrogen bonds: A:F.140, A:S.144, A:H.164, A:E.166, A:E.166, A:T.190 Halogen bonds: A:Q.192 OW1.2: 20 residues within 4Å: Chain B: H.41, M.49, Y.54, F.140, 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.41, B:E.166 Hydrogen bonds: B:F.140, B:S.144, B:H.164, B:E.166, B:E.166, B:T.190 Halogen bonds: B:Q.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brewitz, L. et al., Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine. J.Med.Chem. (2023)

Release Date

2023-02-22

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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