SMTL ID : 8xtd.1

SARS-CoV-2 papain-like-protease (PLpro) in complex with inhibitor Linagliptin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x 356: 8-[(3R)-3-Aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-d ione(Non-covalent)

356.1: 8 residues within 4Å: Chain A: F.69, H.73, N.128, Q.174, H.175, A.176, L.178, D.179 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.69 Hydrogen bonds: A:H.73, A:A.176 Water bridges: A:N.177 pi-Stacking: A:H.73

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.164, Y.264, Y.268, Y.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.164, A:Y.268, A:Y.273 Water bridges: A:V.165 GOL.3: 1 residues within 4Å: Chain A: K.105 No protein-ligand interaction detected (PLIP) GOL.4: 3 residues within 4Å: Chain A: H.89, W.93, D.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.89, A:W.93, A:D.108 GOL.5: 2 residues within 4Å: Chain A: W.106, H.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.272 GOL.6: 6 residues within 4Å: Chain A: W.106, N.109, S.111, Y.112, G.271, H.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.111, A:S.111, A:Y.112 GOL.7: 3 residues within 4Å: Chain A: S.85, N.88, H.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choudhary, S. et al., SARS-CoV-2 papain-like-protease (PLpro) in complex with inhibitor Linagliptin. To Be Published

Release Date

2025-07-16

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

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