SMTL ID : 8uuy.1

SARS-CoV-2 papain-like protease (PLpro) complex with inhibitor Jun12129

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

monomer

Ligands

1 x Y2R: N-{(1R)-1-[(3P,5P)-3-[5-(aminomethyl)thiophen-2-yl]-5-(thiophen-2-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide(Non-covalent)

Y2R.1: 14 residues within 4Å: Chain A: L.165, G.166, D.167, E.170, P.250, P.251, Y.267, G.269, N.270, Y.271, Q.272, Y.276, T.304 Ligands: PGE.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.165, A:D.167, A:P.250, A:P.251, A:Y.267, A:Q.272, A:T.304 Hydrogen bonds: A:D.167, A:Q.272, A:Q.272, A:Y.276 Water bridges: A:D.167, A:R.169 Salt bridges: A:E.170 pi-Stacking: A:Y.271

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

PEG.2: 2 residues within 4Å: Chain A: N.18, E.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.18

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 2 residues within 4Å: Chain A: Y.271 Ligands: Y2R.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.271

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

ACT.4: 3 residues within 4Å: Chain A: N.159, T.161, E.164 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.161 Water bridges: A:N.159

8 x ZN: ZINC ION(Non-covalent)

ZN.5: 2 residues within 4Å: Chain A: K.277, C.287 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.287, H2O.3 ZN.6: 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.7: 3 residues within 4Å: Chain A: H.20, T.66, E.70 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.70 ZN.8: 3 residues within 4Å: Chain A: H.76 Ligands: CL.13, CL.14 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.9: 1 residues within 4Å: Chain A: H.178 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.178, H2O.1, H2O.2 ZN.10: 2 residues within 4Å: Chain A: H.92 Ligands: ZN.11 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, H2O.2 ZN.11: 3 residues within 4Å: Chain A: H.92, D.111 Ligands: ZN.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.111, H2O.2 ZN.12: 2 residues within 4Å: Chain A: C.114, H.275 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.114, A:H.275, H2O.1, H2O.3, H2O.3

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

CL.13: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.8, CL.14 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.8, CL.13 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: F.261, T.262, K.309 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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