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

SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.49, A:N.49, A:S.50 Salt bridges: A:H.48

1 x Y97: 5-(azetidin-3-ylamino)-2-methyl-~{N}-[(1~{R})-1-[3-[5-[[[(3~{R})-oxolan-3-yl]amino]methyl]thiophen-2-yl]phenyl]ethyl]benzamide(Non-covalent)

Y97.4: 12 residues within 4Å: Chain A: L.163, G.164, D.165, E.168, P.249, Y.265, G.267, N.268, Y.269, Q.270, Y.274, T.302 16 PLIP interactions: 16 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:Y.269, A:Q.270, A:T.302 Hydrogen bonds: A:D.165, A:Y.269, A:Q.270, A:Q.270, A:Y.274 Water bridges: A:N.268, A:Y.269

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Chain A: R.167 Ligand excluded by PLIP

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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