SMTL ID : 7qcg.1

Structure of SARS-CoV-2 Papain-like Protease bound to N-(2-pyrrolidyl)-3,4,5-trihydroxybenzoylhydrazone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x DZI: 3,4,5-tris(oxidanyl)-N-[(E)-1H-pyrrol-2-ylmethylideneamino]benzamide(Non-covalent)

DZI.1: 9 residues within 4Å: Chain A: R.166, S.170, Y.171, Q.174, V.202, E.203, M.206, Y.207, M.208 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.174 Hydrogen bonds: A:R.166, A:R.166, A:S.170, A:S.170, A:Q.174, A:E.203, A:E.203, A:M.206, A:M.208 pi-Stacking: A:Y.171

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: S.293, E.295, Y.296, K.297 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.293, A:S.293, A:E.295, A:K.297 Water bridges: A:E.263, A:Y.296, A:K.297 GOL.3: 3 residues within 4Å: Chain A: S.85, N.88, H.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.85, A:H.89

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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

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

CL.5: 4 residues within 4Å: Chain A: K.126, F.127, Q.133, Y.136 Ligand excluded by PLIP

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

PO4.6: 8 residues within 4Å: Chain A: L.162, G.163, D.164, P.248, Y.264, N.267, Y.268, Y.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.273 PO4.7: 2 residues within 4Å: Chain A: K.254, H.255 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.255 Salt bridges: A:K.254, A:H.255 PO4.8: 5 residues within 4Å: Chain A: H.73, N.128, P.129, Q.174, H.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.128 Water bridges: A:A.176, A:A.176 Salt bridges: A:H.73, A:H.175 PO4.9: 2 residues within 4Å: Chain A: H.47, S.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.49

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

2022-03-23

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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