SMTL ID : 9dnu.1

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13296

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x 01: 2-methyl-5-[(1R,5S)-8-methyl-3,8-diazabicyclo[3.2.1]octan-3-yl]-N-{(1R)-1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]ethyl}benzamide

01.1: 12 residues within 4Å: Chain A: L.165, G.166, D.167, R.169, E.170, M.211, P.251, Y.267, Y.271, Q.272, Y.276, T.304 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.167, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Y.271, A:Q.272, A:T.304 Hydrogen bonds: A:D.167, A:R.169, A:Q.272, A:Y.276 Salt bridges: A:E.170 pi-Stacking: A:Y.271, A:Y.271

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

ACT.2: 2 residues within 4Å: Chain A: E.255, E.298 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.257

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 4 residues within 4Å: Chain A: H.76, N.131 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.114, G.274, H.275 Ligands: CL.13 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.114, A:H.275, H2O.2, H2O.7 ZN.6: 3 residues within 4Å: Chain A: H.92, D.111 Ligands: CL.14 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.92, A:D.111 ZN.7: 1 residues within 4Å: Chain A: H.178 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.178, H2O.1, H2O.8, H2O.9, H2O.10 ZN.8: 1 residues within 4Å: Chain A: C.195 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.195 ZN.9: 1 residues within 4Å: Chain A: H.258 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.258, H2O.9, H2O.9, H2O.9 ZN.10: 4 residues within 4Å: Chain A: N.18, H.20, T.66, E.70 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.20, A:E.70

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

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 CL.13: 6 residues within 4Å: Chain A: W.109, N.112, N.113, C.114, H.275 Ligands: ZN.5 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: H.92, K.95, W.96, D.111 Ligands: ZN.6 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jadhav, P. et al., Design of quinoline SARS-CoV-2 papain-like protease inhibitors as oral antiviral drug candidates. Nat Commun (2025)

Release Date

2025-01-22

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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