SMTL ID : 8uuw.1

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12145

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

1 x Y2N: 5-[2-(dimethylamino)ethoxy]-2-methyl-N-{(1R)-1-[(3P,5M)-3-(1-methyl-1H-pyrazol-4-yl)-5-(1,3-thiazol-5-yl)phenyl]ethyl}benzamide(Non-covalent)

Y2N.1: 14 residues within 4Å: Chain A: L.165, G.166, D.167, E.170, M.211, P.250, P.251, Y.267, G.269, N.270, Y.271, Q.272, Y.276, T.304 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.165, A:D.167, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Y.271, A:Y.271, A:Q.272, A:Y.276, A:T.304 Hydrogen bonds: A:D.167, A:Q.272, A:Q.272, A:Y.276 Salt bridges: A:E.170

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 1 residues within 4Å: Chain A: D.43 No protein-ligand interaction detected (PLIP)

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

ACT.3: 2 residues within 4Å: Chain A: N.159, E.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.159

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 1 residues within 4Å: Chain A: C.229 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.229 ZN.5: 3 residues within 4Å: Chain A: H.76 Ligands: CL.10, CL.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.6: 1 residues within 4Å: Chain A: H.258 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.258, H2O.1, H2O.2, H2O.2, H2O.4 ZN.7: 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.1, H2O.3 ZN.8: 3 residues within 4Å: Chain A: W.109, C.114, H.275 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.114, H2O.2, H2O.3

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

CL.9: 4 residues within 4Å: Chain A: T.260, T.262, Y.308, K.309 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: F.72 Ligands: ZN.5 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.5 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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