SMTL ID : 9do5.1

SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12665

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x 01: 5-[2-(dimethylamino)ethoxy]-N-{(1R)-1-[(2P)-2-{1-[2-(dimethylamino)-2-oxoethyl]-1H-pyrazol-4-yl}quinolin-4-yl]ethyl}-2-methylbenzamide

01.1: 12 residues within 4Å: Chain A: G.166, D.167, E.170, M.211, P.251, Y.267, G.269, N.270, Y.271, Q.272, Y.276, T.304 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.167, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Q.272 Hydrogen bonds: A:D.167, A:Y.271, A:Q.272, A:Q.272 Salt bridges: A:E.170 pi-Stacking: A:Y.271, A:Y.271

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 3 residues within 4Å: Chain A: E.255, K.257, E.298 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.257

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.192, C.195, C.227, C.229 Ligands: ZN.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.192, A:C.195, A:C.229 ZN.4: 3 residues within 4Å: Chain A: H.76 Ligands: CL.11, CL.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.5: 3 residues within 4Å: Chain A: H.92, D.111 Ligands: CL.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.92, A:D.111 ZN.6: 5 residues within 4Å: Chain A: C.114, G.274, H.275 Ligands: CL.14, CL.15 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.114, A:H.275 ZN.7: 1 residues within 4Å: Chain A: H.178 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.178, H2O.1, H2O.1, H2O.2, H2O.2 ZN.8: 2 residues within 4Å: Chain A: C.195 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.195 ZN.9: 1 residues within 4Å: Chain A: H.258 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.258, H2O.1, H2O.2, H2O.2 ZN.10: 2 residues within 4Å: Chain A: H.20, E.70 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.20

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

CL.11: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.4, CL.12 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: N.131, P.132, H.178 Ligands: ZN.4, CL.11 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: H.92, K.95, W.96, D.111 Ligands: ZN.5 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: W.109, N.112, C.114, H.275 Ligands: ZN.6 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: G.274, H.275 Ligands: ZN.6 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: F.261, T.262, K.309 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 2 residues within 4Å: Chain A: D.43, K.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.43, A:K.46 GOL.18: 2 residues within 4Å: Chain A: H.275, D.289 No protein-ligand interaction detected (PLIP) GOL.19: 4 residues within 4Å: Chain A: N.159, K.160, T.161, E.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.160, A:T.161, A:E.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ansari, A. et al., SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12665. 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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