SMTL ID : 8uug.1

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12303

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

monomer

Ligands

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

XXW.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:D.167, A:D.167, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Y.271, A:Q.272 Hydrogen bonds: A:D.167, A:R.169, A:Y.271, A:Q.272, A:Q.272, A:Y.276 Salt bridges: A:E.170 pi-Stacking: A:Y.271

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: W.109, H.275, D.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.289

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

ACT.3: 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 Hydrogen bonds: A:E.164

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.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, C.114, G.274, H.275 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.114, A:H.275, H2O.5 ZN.7: 3 residues within 4Å: Chain A: H.92, K.95 Ligands: ZN.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.92 ZN.8: 4 residues within 4Å: Chain A: H.92, D.111, V.162 Ligands: ZN.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.92, A:D.111

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

CL.9: 4 residues within 4Å: Chain A: F.261, T.262, Y.308, K.309 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.4, CL.12 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.4, 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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