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

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-83

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.190, T.192, C.193, C.225, C.227 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.190, A:C.193, A:C.225, A:C.227

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

SO4.2: 5 residues within 4Å: Chain A: H.74, N.129, P.130, Q.175, H.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.129 Salt bridges: A:H.74, A:H.176 SO4.5: 3 residues within 4Å: Chain A: H.48, N.49, S.50 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.49, A:N.49, A:S.50, A:S.50 Salt bridges: A:H.48 SO4.6: 1 residues within 4Å: Chain A: R.141 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.141 SO4.8: 4 residues within 4Å: Chain A: T.266, G.267, P.300 Ligands: Y54.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.267

2 x BO3: BORIC ACID(Non-covalent)

BO3.3: 3 residues within 4Å: Chain A: E.125, E.308, N.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.309 BO3.4: 7 residues within 4Å: Chain A: P.60, A.69, T.75, T.76, D.77, F.80, L.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.75, A:F.80, A:L.81

1 x Y54: 5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1R,3S)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide(Non-covalent)

Y54.7: 12 residues within 4Å: Chain A: L.163, G.164, D.165, E.168, P.249, Y.265, G.267, Y.269, Q.270, Y.274, T.302 Ligands: SO4.8 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.163, A:D.165, A:P.249, A:P.249, A:Y.265, A:Q.270 Hydrogen bonds: A:D.165, A:D.165, A:E.168, A:Q.270 pi-Stacking: A:Y.269, A:Y.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Z. et al., Potent, Novel SARS-CoV-2 PLpro Inhibitors Block Viral Replication in Monkey and Human Cell Cultures. Biorxiv (2021)

Release Date

2021-02-24

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

Related Entries With Identical Sequence