SMTL ID : 8uuh.1

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12199

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x XYI: 5-[2-(dimethylamino)ethoxy]-2-methyl-N-[(1R)-1-{(3M,5P)-3-(1-methyl-1H-pyrazol-4-yl)-5-[1-(propan-2-yl)-1H-pyrazol-4-yl]phenyl}ethyl]benzamide(Non-covalent)

XYI.1: 15 residues within 4Å: Chain A: L.165, G.166, D.167, R.169, E.170, M.211, P.250, P.251, Y.267, G.269, N.270, Y.271, Q.272, Y.276, T.304 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.251, A:Y.267, A:Y.267, A:Y.267, A:Y.271, A:Q.272 Hydrogen bonds: A:D.167, A:Q.272, A:Q.272, A:Y.276 Salt bridges: A:E.170 pi-Stacking: A:Y.271

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: W.109, H.275, D.289 No protein-ligand interaction detected (PLIP) PEG.3: 3 residues within 4Å: Chain A: T.66, E.70, E.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.70

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.192, C.195, C.227, C.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.192, A:C.195, A:C.227, A:C.229 ZN.5: 3 residues within 4Å: Chain A: H.76 Ligands: CL.11, CL.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.6: 3 residues within 4Å: Chain A: H.92, D.111 Ligands: ZN.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.92, A:D.111 ZN.7: 3 residues within 4Å: Chain A: H.92, K.95 Ligands: ZN.6 No protein-ligand interaction detected (PLIP) ZN.8: 4 residues within 4Å: Chain A: W.109, C.114, G.274, H.275 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.114, A:H.275, H2O.1, H2O.2

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain A: T.262, Y.308, K.309 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.5, CL.12 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.5, CL.11 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, B. et al., Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. Science (2024)

Release Date

2024-04-03

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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