SMTL ID : 9d2k.1 (1 other biounit)

SARS-CoV-2 Papain-like Protease (PLpro) complex with covalent inhibitor Jun13567

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x 01: 2-(3-{2-[4-(3,3-dimethylazetidin-1-yl)-4-oxobutanoyl]hydrazin-1-yl}-3-oxopropyl)-N-{(1R)-1-[(3P,5P)-3-(1-ethyl-1H-pyrazol-3-yl)-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}benzamide

01.1: 21 residues within 4Å: Chain A: W.109, N.112, N.113, C.114, Y.115, L.165, G.166, D.167, E.170, M.211, P.251, Y.267, G.269, N.270, Y.271, Q.272, C.273, G.274, H.275, Y.276, T.304 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.165, A:L.165, A:D.167, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Y.271 Hydrogen bonds: A:C.114, A:G.166, A:G.166, A:D.167, A:Y.271, A:Q.272, A:G.274, A:G.274, A:Y.276

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.2: 3 residues within 4Å: Chain A: C.195, C.227, T.228 No protein-ligand interaction detected (PLIP)

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.76, N.131 Ligands: CL.8, CL.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.4: 2 residues within 4Å: Chain A: H.92 Ligands: CL.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.92 ZN.5: 2 residues within 4Å: Chain A: H.258 Ligands: CL.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.258 ZN.6: 2 residues within 4Å: Chain A: H.275, D.289 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.275, A:D.289 ZN.7: 4 residues within 4Å: Chain A: C.192, C.195, C.227, C.229 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.192, A:C.227, A:C.229

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

CL.8: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.3, CL.9 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.3, CL.8 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: W.96, D.111 Ligands: ZN.4 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: F.261, T.262, Y.308, K.309 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: H.258, E.283 Ligands: ZN.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, B. et al., Structure-Based Design of Covalent SARS-CoV-2 Papain-like Protease Inhibitors. J.Med.Chem. (2024)

Release Date

2025-03-26

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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