SMTL ID : 7nt4.1 (1 other biounit)

X-ray structure of SCoV2-PLpro in complex with small molecule inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

monomer

Ligands

3 x PRL: PROFLAVIN(Non-covalent)

PRL.1: 6 residues within 4Å: Chain A: G.166, D.167, Y.267, Y.271, Y.276 Ligands: PRL.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.167, A:Y.267, A:Y.271 Hydrogen bonds: A:G.166, A:D.167 pi-Stacking: A:Y.271 PRL.2: 9 residues within 4Å: Chain A: D.167, M.211, P.250, P.251, Y.267, Y.271, Y.276, T.304 Ligands: PRL.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.250, A:P.251, A:Y.271 Hydrogen bonds: A:Y.276 Water bridges: A:R.169 pi-Stacking: A:Y.267 PRL.3: 5 residues within 4Å: Chain A: W.109, T.268, C.273, G.274, H.275 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.275 Water bridges: A:H.275, A:D.289 pi-Stacking: A:H.275

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 12 residues within 4Å: Chain A: C.114, A.117, T.118, L.121, H.275, Y.276, K.277, H.278, I.288, D.289, G.290 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.275, A:G.290 EDO.5: 10 residues within 4Å: Chain A: I.107, K.108, W.109, N.113, C.114, A.117, H.275, D.289, G.290 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.275 Water bridges: A:W.109 EDO.6: 3 residues within 4Å: Chain A: L.293, T.294, K.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.295 EDO.7: 6 residues within 4Å: Chain A: G.259, T.260, F.261, T.262, Y.308, K.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.259, A:K.309

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: C.192, C.195, C.227, C.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.192, A:C.195, A:C.227, A:C.229

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 4 residues within 4Å: Chain A: K.295, S.296, S.297, E.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.295, A:S.297, A:E.298 SO4.10: 1 residues within 4Å: Chain A: K.257 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Napolitano, V. et al., Acriflavine, a clinically approved drug, inhibits SARS-CoV-2 and other betacoronaviruses. Cell Chem Biol (2022)

Release Date

2022-02-02

Peptides

Non-structural protein 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 3

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