SMTL ID : 8yx5.1 (1 other biounit)

Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-P35

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

1 x 01: 5-[(1~{R},5~{S})-3,6-diazabicyclo[3.1.1]heptan-3-yl]-2-methyl-~{N}-[1-(1-methyl-2-oxidanylidene-benzo[cd]indol-6-yl)cyclopropyl]benzamide

01.1: 13 residues within 4Å: Chain A: K.158, L.163, G.164, D.165, E.168, M.209, P.248, P.249, Y.265, Y.269, Q.270, Y.274, T.302 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.163, A:D.165, A:P.248, A:P.248, A:P.249, A:Y.265, A:Y.265, A:Y.265, A:Q.270, A:T.302 Hydrogen bonds: A:D.165, A:Y.265, A:Q.270 Water bridges: A:K.158 Salt bridges: A:E.168 pi-Stacking: A:Y.269, A:Y.269, A:Y.269

2 x ZN: ZINC ION(Non-functional Binders)(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: A.231 No protein-ligand interaction detected (PLIP) ZN.3: 5 residues within 4Å: Chain A: W.107, N.110, S.112, L.163, H.273 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.112

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 11 residues within 4Å: Chain A: S.213, Y.214, E.215, Y.252, E.253, L.254, K.255, T.258, F.259, V.304, Y.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.253, A:K.255 Water bridges: A:Y.214 GOL.5: 7 residues within 4Å: Chain A: G.257, T.258, F.259, T.260, F.305, Y.306, K.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.258, A:K.307, A:K.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, Y. et al., Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19. Nat Commun (2024)

Release Date

2024-12-04

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

Related Entries With Identical Sequence