SMTL ID : 8uuu.1

SARS-Cov-2 papain-like protease (PLpro) with inhibitor Jun12162

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

monomer

Ligands

1 x XYR: N-{(1R)-1-[(3P,5M)-3-[1-(difluoromethyl)-1H-pyrazol-4-yl]-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide(Non-covalent)

XYR.1: 15 residues within 4Å: Chain A: L.165, G.166, D.167, R.169, E.170, M.211, P.250, P.251, Y.267, G.269, N.270, Y.271, Q.272, Y.276, T.304 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.167, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Q.272 Hydrogen bonds: A:D.167, A:Q.272, A:Q.272, A:Y.276 Salt bridges: A:E.170 pi-Stacking: A:Y.271

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 2 residues within 4Å: Chain A: N.159, E.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.159

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: W.109, C.114, H.275 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.114, A:H.275, H2O.2, H2O.3 ZN.4: 3 residues within 4Å: Chain A: H.76 Ligands: CL.10, CL.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.5: 4 residues within 4Å: Chain A: C.192, C.195, C.227, T.228 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.195, A:C.227 ZN.6: 3 residues within 4Å: Chain A: H.92, D.111 Ligands: ZN.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.92, A:D.111 ZN.7: 4 residues within 4Å: Chain A: H.92, K.95, D.111 Ligands: ZN.6 No protein-ligand interaction detected (PLIP) ZN.8: 3 residues within 4Å: Chain A: N.18, H.20, E.70 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.20, A:E.70

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

CL.9: 4 residues within 4Å: Chain A: F.261, T.262, Y.308, K.309 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.4, CL.11 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.4, CL.10 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 3 residues within 4Å: Chain A: W.109, H.275, D.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.275 GOL.13: 3 residues within 4Å: Chain A: E.255, K.257, E.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.257, A:E.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, B. et al., Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. Science (2024)

Release Date

2024-04-03

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