SMTL ID : 7qch.1

Structure of SARS-CoV-2 Papain-like Protease bound to N-(3,5-dimethoxy-4-hydroxybenzyliden)thiosemicarbazone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x A5I: N-(3,5-dimetoxy-4-hydroxybenzyliden)thiosemicarbazone(Non-covalent)

A5I.1: 13 residues within 4Å: Chain A: L.58, P.59, R.65, A.68, F.69, Y.72, T.74, T.75, D.76, P.77, S.78, F.79, L.80 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.59, A:A.68 Hydrogen bonds: A:R.65, A:D.76, A:F.79, A:L.80 Water bridges: A:G.81

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: L.162, G.163, D.164, P.247, P.248, Y.264, N.267, Y.268, Y.273, T.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.164, A:Y.273 GOL.3: 6 residues within 4Å: Chain A: T.9, H.17, Q.19, D.61, T.63, L.64 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.63 Water bridges: A:H.17, A:Q.19, A:T.63

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.189, T.191, C.192, C.224, C.226 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.189, A:C.192, A:C.224, A:C.226

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: H.73, N.128, P.129, Q.174, H.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.128 Salt bridges: A:H.73, A:H.175 PO4.6: 3 residues within 4Å: Chain A: S.85, N.88, H.89 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.89 PO4.7: 2 residues within 4Å: Chain A: H.47, S.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.49, A:S.49 Salt bridges: A:H.47 PO4.8: 1 residues within 4Å: Chain A: H.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.294 Salt bridges: A:H.255 PO4.9: 6 residues within 4Å: Chain A: H.89, K.92, W.93, A.107, D.108, V.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.93, A:D.108, A:D.108 Salt bridges: A:H.89

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

CL.10: 4 residues within 4Å: Chain A: K.126, F.127, Q.133, Y.136 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ewert, W. et al., Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease. Front Chem (2022)

Release Date

2022-03-16

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