SMTL ID : 7jiw.1

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x VBY: 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide(Non-covalent)

VBY.1: 11 residues within 4Å: Chain A: L.165, G.166, D.167, E.170, 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.250, A:P.251, A:Y.267, A:Y.267, A:Y.267, A:Y.271, A:T.304 Hydrogen bonds: A:D.167, A:E.170, A:Q.272, A:Q.272, A:Y.276 pi-Stacking: A:Y.271, A:Y.271

4 x ZN: ZINC ION(Non-covalent)

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

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

CL.6: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.4, CL.7 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.4, CL.6 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: W.109, N.112, N.113, C.114, H.275 Ligands: ZN.5 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: H.92, K.95 Ligands: ZN.3 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.10: 6 residues within 4Å: Chain A: K.108, W.109, D.289, G.290, A.291, L.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.109, A:A.291, A:L.292 Salt bridges: A:D.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun (2021)

Release Date

2020-08-05

Peptides

Papain-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease

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