SMTL ID : 8uuf.1

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun11941

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

monomer

Ligands

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

XWO.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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.165, A:D.167, A:P.251, A:Y.267, A:Y.267, A:Y.271 Hydrogen bonds: A:D.167, A:Q.272, A:Q.272, A:Y.276 Salt bridges: A:E.170 pi-Stacking: A:Y.271

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 1 residues within 4Å: Chain A: H.258 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.258

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.76 Ligands: CL.9, CL.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.4: 2 residues within 4Å: Chain A: H.92, D.111 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.92, A:D.111, H2O.2, H2O.3 ZN.5: 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.6: 4 residues within 4Å: Chain A: W.109, N.112, C.114, H.275 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.114, A:H.275

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

CL.7: 4 residues within 4Å: Chain A: F.261, T.262, Y.308, K.309 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: H.20, D.64 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.3, CL.10 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.3, CL.9 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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