SMTL ID : 8iho.1

Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x PQX- GLY- GLY- GVE: covalent inhibitor(Non-covalent)

PQX-GLY-GLY-GVE.1: 19 residues within 4Å: Chain A: W.107, N.110, C.112, Y.113, L.163, G.164, D.165, P.249, Y.265, N.268, Y.269, Q.270, C.271, G.272, H.273, Y.274, D.287, T.302 Ligands: PQX-GLY-GLY-GVE.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.165, A:P.249, A:Y.265, A:Y.269, A:Y.269 Hydrogen bonds: A:N.110, A:G.164, A:G.164, A:Y.265, A:Y.269, A:G.272 Salt bridges: A:D.165, A:H.273 pi-Stacking: A:Y.269, A:Y.269 PQX-GLY-GLY-GVE.2: 18 residues within 4Å: Chain A: P.248 Chain B: W.107, N.110, C.112, Y.113, L.163, G.164, D.165, P.248, P.249, Y.265, N.268, Y.269, C.271, G.272, H.273, Y.274 Ligands: PQX-GLY-GLY-GVE.1 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.110, B:P.248, B:P.249, B:Y.265, B:Y.265, B:Y.269, A:P.248 Hydrogen bonds: B:N.110, B:Y.113, B:G.164, B:G.164, B:Y.269, B:G.272 Salt bridges: B:D.165, B:H.273 pi-Stacking: B:Y.269

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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 ZN.4: 4 residues within 4Å: Chain B: C.190, C.193, C.225, C.227 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.190, B:C.193, B:C.225, B:C.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Structure-Based Design of Potent Peptidomimetic Inhibitors Covalently Targeting SARS-CoV-2 Papain-like Protease. Int J Mol Sci (2023)

Release Date

2024-01-03

Peptides

Papain-like protease nsp3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Papain-like protease nsp3