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

Crystal structure of the wild type SARS-CoV-2 papain-like protease (PLPro) with inhibitor GRL0617

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

monomer

Ligands

1 x TTT: 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide(Non-covalent)

TTT.1: 11 residues within 4Å: Chain A: L.162, G.163, D.164, E.167, P.247, P.248, Y.264, Y.268, Q.269, Y.273, T.301 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.162, A:D.164, A:P.247, A:P.248, A:Y.264, A:Y.264, A:Y.264, A:Y.268, A:Y.273, A:T.301 Hydrogen bonds: A:D.164, A:D.164, A:Y.268, A:Q.269 pi-Stacking: A:Y.268, A:Y.268

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.189, C.192, C.224, C.226 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.189, A:C.192, A:C.224

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: K.182, K.200 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.182, A:K.200 SO4.4: 2 residues within 4Å: Chain A: T.265, G.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, C. et al., Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay. Acs Cent.Sci. (2021)

Release Date

2020-08-26

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

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