SMTL ID : 7qcm.1

Structure of SARS-CoV-2 Papain-like Protease bound to N-(3-methoxy-4-hydroxy-acetophenone)thiosemicarbazone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

1 x A3X: N-(3-metoxy-4-hydroxy-acetophenone)thiosemicarbazone(Non-covalent)

A3X.1: 15 residues within 4Å: Chain A: L.58, P.59, L.64, R.65, V.66, A.68, F.69, T.74, T.75, D.76, P.77, S.78, F.79, L.80 Ligands: PO4.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.59, A:R.65, A:A.68 Hydrogen bonds: A:D.76, A:F.79, A:L.80 Water bridges: A:R.65, A:R.65, A:T.75, A:G.81

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: T.9, H.17, Q.19, D.61, T.63, L.64 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.17, A:T.63, A:T.63 GOL.3: 3 residues within 4Å: Chain A: S.85, N.88, H.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.85, A:S.85, A:H.89 GOL.4: 3 residues within 4Å: Chain A: Q.133, D.134, Y.137 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.130, A:Q.133, A:Q.133 GOL.5: 3 residues within 4Å: Chain A: H.47, N.48, S.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.47, A:N.48, A:S.49, A:S.49 GOL.6: 10 residues within 4Å: Chain A: T.9, H.17, Q.19, Q.30, F.31, V.57, N.60, D.61, L.64 Ligands: GOL.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.9, A:T.9, A:Q.19, A:Q.30, A:N.60

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: C.189, T.191, C.192, C.224, C.226, K.228 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.189, A:C.192, A:C.224, A:C.226

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

CL.8: 4 residues within 4Å: Chain A: K.126, F.127, Q.133, Y.136 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: Y.296, K.297 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: H.89, W.93, D.108 Ligand excluded by PLIP

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

PO4.11: 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 PO4.12: 2 residues within 4Å: Chain A: P.77 Ligands: A3X.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.65 PO4.13: 2 residues within 4Å: Chain A: H.255, E.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.295 Water bridges: A:H.255 Salt bridges: A:H.255

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

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