SMTL ID : 8h6n.1

Crystal structure of SARS-CoV-2 main protease (Mpro) Mutant (T21I) in complex with protease inhibitor Nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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: 21 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, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.41, A:E.166 Hydrogen bonds: A:G.143, A:C.145, A:H.164, A:E.166, A:E.166, A:T.190, B:S.1 Halogen bonds: A:Q.192 Water bridges: B:S.1 4WI.3: 21 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, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.41, B:E.166 Hydrogen bonds: B:G.143, B:C.145, B:H.164, B:E.166, B:E.166, B:T.190, A:S.1 Halogen bonds: B:Q.192 Water bridges: A:S.1

2 x LQZ: 2-(diethylamino)-N-(2,6-dimethylphenyl)ethanamide(Non-covalent)

LQZ.2: 5 residues within 4Å: Chain A: T.98, P.99, K.100, Y.101, K.102 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.98, A:K.100, A:K.100, A:Y.101, A:Y.101 Hydrogen bonds: A:Y.101 LQZ.4: 5 residues within 4Å: Chain B: T.98, P.99, K.100, Y.101, K.102 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.98, B:K.100, B:K.100, B:Y.101, B:Y.101 Hydrogen bonds: B:Y.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, Y. et al., Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature (2023)

Release Date

2023-10-11

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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