SMTL ID : 9cjp.1

X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 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, Y.54, F.140, L.141, N.142, G.143, A.144, C.145, H.163, H.164, M.165, V.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 Chain B: S.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.41, A:M.165 Hydrogen bonds: A:F.140, A:G.143, A:C.145, A:H.164, A:V.166, A:V.166, A:T.190, B:S.1 4WI.4: 21 residues within 4Å: Chain A: S.1 Chain B: H.41, Y.54, F.140, L.141, N.142, G.143, A.144, C.145, H.163, H.164, M.165, V.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.41, B:M.165 Hydrogen bonds: B:G.143, B:C.145, B:H.164, B:V.166, B:V.166, B:T.190, A:S.1, A:S.1

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: S.121, P.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.121, A:S.121 EDO.5: 3 residues within 4Å: Chain A: S.123 Chain B: R.298, S.301 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.301

3 x BR: BROMIDE ION(Non-covalent)

BR.3: 2 residues within 4Å: Chain A: R.4, K.5 Ligand excluded by PLIP BR.6: 2 residues within 4Å: Chain B: T.226, N.228 Ligand excluded by PLIP BR.7: 2 residues within 4Å: Chain B: W.218, R.279 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain B: D.33, T.98, P.99, K.100 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esler, M.A. et al., X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir. To Be Published

Release Date

2025-07-09

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5

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