SMTL ID : 8uob.1

SARS-CoV-2 Papain-like protease (PLpro) with Inhibitor Jun12682

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

monomer

Ligands

1 x XB5: 5-[2-(dimethylamino)ethoxy]-N-{(1R)-1-[(3M,5P)-3-(1-ethyl-1H-pyrazol-3-yl)-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}-2-methylbenzamide(Non-covalent)

XB5.1: 13 residues within 4Å: Chain A: L.165, G.166, D.167, E.170, M.211, P.250, P.251, Y.267, G.269, Y.271, Q.272, Y.276, T.304 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.167, A:P.251, 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

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 3 residues within 4Å: Chain A: H.76 Ligands: CL.8, CL.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.4: 3 residues within 4Å: Chain A: H.92, D.111 Ligands: ZN.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:D.111, H2O.7 ZN.5: 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.6 ZN.6: 3 residues within 4Å: Chain A: H.92, D.111 Ligands: ZN.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, H2O.7 ZN.7: 3 residues within 4Å: Chain A: N.18, H.20, E.70 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.20, A:E.70

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

CL.8: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.3, CL.9 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.3, CL.8 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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