SMTL ID : 8yx4.1

Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-P31

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

1 x 01: 2-methyl-~{N}-[1-(1-methyl-2-oxidanylidene-benzo[cd]indol-6-yl)cyclopropyl]-5-[3-(4-methyl-4-oxidanyl-piperidin-1-yl)azetidin-1-yl]benzamide

01.1: 13 residues within 4Å: Chain A: K.158, L.163, G.164, D.165, E.168, M.209, P.248, P.249, Y.265, Y.269, Q.270, Y.274, T.302 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:D.165, A:P.248, A:P.248, A:P.249, A:Y.265, A:Y.265, A:Y.265, A:Y.269, A:Q.270 Hydrogen bonds: A:D.165, A:Y.265, A:Q.270 Salt bridges: A:E.168 pi-Stacking: A:Y.269, A:Y.269, A:Y.269

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: S.213, Y.252, E.253, L.254, K.255, T.258, F.259, V.304, Y.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.252, A:K.255, A:T.258 Water bridges: A:Y.214

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: E.264, K.275, I.277, C.285, Y.297 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.264, A:C.285, H2O.4 ZN.4: 5 residues within 4Å: Chain A: C.190, T.192, C.193, C.225, C.227 No protein-ligand interaction detected (PLIP) ZN.5: 5 residues within 4Å: Chain A: S.181, C.182, E.239, S.240, P.241 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.181, A:S.181

6 x CD: CADMIUM ION(Non-covalent)

CD.6: 4 residues within 4Å: Chain A: H.74, N.129 Ligands: CL.12, CL.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.74 CD.7: 2 residues within 4Å: Chain A: Y.155, H.176 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.176, H2O.5 CD.8: 1 residues within 4Å: Chain A: H.256 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.256 CD.9: 5 residues within 4Å: Chain A: W.107, N.110, S.112, G.272, H.273 No protein-ligand interaction detected (PLIP) CD.10: 3 residues within 4Å: Chain A: C.271 Ligands: CD.11, CL.14 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.271 CD.11: 3 residues within 4Å: Chain A: N.268, C.271 Ligands: CD.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.271, H2O.3

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

CL.12: 3 residues within 4Å: Chain A: F.70, H.74 Ligands: CD.6 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: H.74, N.129, P.130, H.176 Ligands: CD.6 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Ligands: CD.10 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, Y. et al., Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19. Nat Commun (2024)

Release Date

2024-12-04

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3

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