SMTL ID : 9do1.1

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13307

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x 01: 2-methyl-N-{(1R)-1-[(2M)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]ethyl}-5-{[(2R)-1-methylpyrrolidin-2-yl]methoxy}benzamide

01.1: 13 residues within 4Å: Chain A: L.165, G.166, D.167, R.169, E.170, M.211, P.250, P.251, Y.267, Y.271, Q.272, Y.276, T.304 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.167, A:P.251, A:Y.267, A:Y.267, A:Q.272, A:T.304 Hydrogen bonds: A:D.167, A:Q.272, A:Q.272, A:Y.276 Water bridges: A:K.160 Salt bridges: A:E.170 pi-Stacking: A:Y.271, A:Y.271, A:Y.271

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: W.109, H.275, D.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.289 Water bridges: A:A.291

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 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 ZN.4: 3 residues within 4Å: Chain A: H.76 Ligands: CL.9, CL.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.5: 2 residues within 4Å: Chain A: H.92, D.111 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:D.111, H2O.7 ZN.6: 3 residues within 4Å: Chain A: H.178 Ligands: CL.11, CL.12 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.178, H2O.8 ZN.7: 1 residues within 4Å: Chain A: C.195 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.195 ZN.8: 4 residues within 4Å: Chain A: C.114, G.274, H.275 Ligands: CL.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.114, A:H.275

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

CL.9: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.4, CL.10 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.4, CL.9 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: H.76, H.178 Ligands: ZN.6 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: Y.157, Y.174, H.178 Ligands: ZN.6 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: N.112, C.114, H.275 Ligands: ZN.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ansari, A. et al., SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13307. To Be Published

Release Date

2025-01-22

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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