SMTL ID : 9cyc.2 (1 other biounit)

SARS-CoV-2 PLpro in complex with inhibitor WEHI-P2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x 01: (E)-1-[(3R)-1-cyclopentylpiperidin-3-yl]-N-methoxy-1-(6-methoxynaphthalen-2-yl)methanimine

01.1: 13 residues within 4Å: Chain A: L.165, G.166, D.167, R.169, M.211, G.212, S.248, A.249, P.250, P.251, Y.267, Y.276, T.304 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.167, A:P.250, A:P.251, A:Y.267, A:Y.267 Salt bridges: A:D.167

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 9 residues within 4Å: Chain A: W.109, N.112, N.113, S.114, Y.115, L.165, G.274, H.275, Y.276 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.112, A:L.165 Hydrogen bonds: A:W.109, A:S.114, A:Y.115 Water bridges: A:G.166, A:H.275

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.92, K.95, W.96, A.110, D.111, V.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

M Bader, S. et al., A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID. Nat Commun (2025)

Release Date

2025-04-09

Peptides

Papain-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Papain-like protease

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