SMTL ID : 7tzj.1 (1 other biounit)

SARS CoV-2 PLpro in complex with inhibitor 3k

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

monomer

Ligands

1 x S88: N-[(3-fluorophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide(Non-covalent)

S88.1: 14 residues within 4Å: Chain A: L.165, G.166, D.167, M.211, P.250, P.251, Y.267, G.269, N.270, Y.271, Q.272, Y.276, T.304 Ligands: DMS.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.250, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Y.271, A:Y.271, A:Q.272, A:T.304 Hydrogen bonds: A:Y.271 Salt bridges: A:D.167 pi-Stacking: A:Y.271, A:Y.271

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: H.50 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.50 ZN.3: 2 residues within 4Å: Chain A: H.92, D.111 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.92 ZN.4: 1 residues within 4Å: Chain A: H.76 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.76, H2O.1, H2O.1 ZN.5: 2 residues within 4Å: Chain A: H.20, E.70 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.20, A:E.70, H2O.1

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

DMS.6: 7 residues within 4Å: Chain A: K.160, L.165, G.166, D.167, E.170, Y.271 Ligands: S88.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.160 Salt bridges: A:E.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calleja, D.J. et al., Insights Into Drug Repurposing, as Well as Specificity and Compound Properties of Piperidine-Based SARS-CoV-2 PLpro Inhibitors. Front Chem (2022)

Release Date

2022-03-02

Peptides

Papain-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease

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