SMTL ID : 8z4w.3 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

monomer

Ligands

1 x 01: 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone

01.1: 9 residues within 4Å: Chain A: W.107, N.110, N.111, C.112, L.163, N.268, C.271, G.272, H.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.110, A:C.112 Water bridges: A:Y.113

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: Y.252, E.253, L.254, K.255, T.258, F.259, Y.306 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.252, A:K.255, A:K.255, A:T.258, A:Y.306, A:Y.306 GOL.3: 9 residues within 4Å: Chain A: P.60, A.69, F.70, Y.73, T.75, D.77, P.78, F.80, L.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.69, A:F.80, A:L.81

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, X. et al., Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Nonstructural Protein Inhibitors. J.Am.Chem.Soc. (2024)

Release Date

2025-02-26

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Non-structural protein 3

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