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

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-24

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x XR8: 5-[(azetidin-3-yl)amino]-2-methyl-N-[(1R)-1-(3-{5-[(pyrrolidin-1-yl)methyl]thiophen-2-yl}phenyl)ethyl]benzamide(Non-covalent)

XR8.1: 11 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.163, A:D.165, A:P.249, A:Y.265, A:Y.265, A:Y.269, A:Q.270, A:T.302 Hydrogen bonds: A:D.165, A:E.168, A:Q.270, A:Q.270 pi-Stacking: A:Y.269

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: C.190, C.193, C.225 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.190, A:C.193, A:C.225

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

SO4.3: 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 SO4.7: 3 residues within 4Å: Chain A: H.48, N.49, S.50 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.49, A:N.49, A:S.50 Salt bridges: A:H.48

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: P.60, T.75, T.76, D.77, P.78, L.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.75, A:L.81 GOL.5: 6 residues within 4Å: Chain A: Y.252, E.253, L.254, K.255, T.258, Y.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.255, A:T.258, A:T.258, A:Y.306

1 x BO3: BORIC ACID(Non-covalent)

BO3.6: 2 residues within 4Å: Chain A: D.38, N.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.38, A:N.147

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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