SMTL ID : 8wti.1

Crystal structure of the SARS-CoV-2 main protease in complex with 20j

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x X1Z: ~{N}-[(1~{R})-1-cyclohexyl-2-[[(2~{R})-3-methoxy-1-oxidanylidene-1-[[1-[(1~{S})-1-oxidanyl-2-oxidanylidene-2-(1,3-thiazol-2-ylmethylamino)ethyl]cyclobutyl]amino]propan-2-yl]amino]-2-oxidanylidene-ethyl]-4,4-bis(fluoranyl)cyclohexane-1-carboxamide

X1Z.1: 21 residues within 4Å: Chain A: T.25, T.26, 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, D.187, R.188, Q.189, T.190, Q.192 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.25, A:M.49, A:M.165 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164 Water bridges: A:E.166 Halogen bonds: A:T.190, A:Q.192 X1Z.5: 22 residues within 4Å: Chain B: T.25, T.26, H.41, S.46, 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, D.187, R.188, Q.189, T.190, Q.192 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.25, B:M.49, B:M.165 Hydrogen bonds: B:S.46, B:G.143, B:S.144, B:C.145, B:H.164 Water bridges: B:S.46, B:E.166, B:Q.189 Halogen bonds: B:T.190, B:Q.192

2 x PEG: DI(HYDROXYETHYL)ETHER

PEG.2: 1 residues within 4Å: Chain A: K.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.90 PEG.3: 4 residues within 4Å: Chain A: R.4, K.5 Chain B: R.4, K.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.4, B:K.5, A:R.4, A:R.4, A:K.5 Water bridges: B:F.3

1 x SO4: SULFATE ION

SO4.4: 2 residues within 4Å: Chain A: K.97 Chain B: K.97 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.97, B:K.97 Water bridges: B:K.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Q. et al., Discovery of alpha-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups. Bioorg.Chem. (2024)

Release Date

2024-08-28

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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