SMTL ID : 7lbr.2 (1 other biounit)

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-89

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.190, 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

2 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.129, A:Q.175 Salt bridges: A:H.74, A:H.176 SO4.3: 3 residues within 4Å: Chain A: H.48, N.49, S.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.49, A:S.50 Salt bridges: A:H.48

1 x XT7: 5-[(azetidin-3-yl)amino]-N-[(1R)-1-{3-[5-({[(1S,3R)-3-hydroxycyclopentyl]amino}methyl)thiophen-2-yl]phenyl}ethyl]-2-methylbenzamide(Non-covalent)

XT7.4: 13 residues within 4Å: Chain A: K.158, L.163, G.164, D.165, E.168, P.249, Y.265, G.267, N.268, Y.269, Q.270, Y.274, T.302 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.163, A:D.165, A:P.249, A:Y.265, A:Y.269, A:Q.270, A:Q.270, A:T.302 Hydrogen bonds: A:D.165, A:Y.269, A:Q.270, A:Q.270, A:Y.274 pi-Stacking: A:Y.269

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.125, P.241, E.308, N.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.309 Water bridges: A:P.241, A:K.307

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
B

Non-structural protein 3

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