SMTL ID : 9cyk.1

SARS-CoV-2 PLpro in complex with inhibitor WEHI-P24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x 01: {(3R)-1-[(1s,4S)-4-hydroxycyclohexyl]piperidin-3-yl}(6-methoxynaphthalen-2-yl)methanone

01.1: 20 residues within 4Å: Chain A: K.160, 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 Chain B: L.188, V.190, Q.198, Q.199, T.200, Y.236 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.250, A:P.251, A:Y.267, B:V.190, B:T.200 Hydrogen bonds: A:L.165, A:Y.276, B:Q.199 Salt bridges: A:D.167 01.4: 20 residues within 4Å: Chain A: L.188, V.190, Q.198, Q.199, T.200, Y.236 Chain B: K.160, 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 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.250, B:P.251, B:Y.267, A:V.190, A:T.200 Hydrogen bonds: B:Y.276, A:Q.199 Salt bridges: B:D.167

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

ACY.2: 7 residues within 4Å: Chain A: W.109, N.112, N.113, S.114, L.165, G.274, H.275 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.112 Hydrogen bonds: A:W.109, A:N.112, A:S.114, A:S.114 Water bridges: A:Y.115 Salt bridges: A:H.275 ACY.5: 8 residues within 4Å: Chain B: W.109, N.112, N.113, S.114, L.165, C.273, G.274, H.275 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.112, B:L.165 Hydrogen bonds: B:W.109, B:N.112, B:S.114, B:S.114 Salt bridges: B:H.275

2 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.92, A:W.96 Water bridges: A:D.111, A:D.111 GOL.6: 6 residues within 4Å: Chain B: H.92, K.95, W.96, A.110, D.111, V.162 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.92, B:D.111 Water bridges: B:K.95, B:D.111

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Papain-like protease

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