SMTL ID : 7jn2.1

The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder441 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

1 x Y41: 3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide(Non-covalent)

Y41.1: 9 residues within 4Å: Chain A: L.165, G.166, D.167, P.251, Y.267, 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, A:T.304 Hydrogen bonds: A:D.167, A:E.170, A:Q.272, A:Y.276 pi-Stacking: A:Y.271, A:Y.271

5 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: 4 residues within 4Å: Chain A: N.18, H.20, T.66, E.70 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.20, A:H.20, A:E.70, A:E.70 ZN.4: 2 residues within 4Å: Chain A: H.92, D.111 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.92, A:D.111, H2O.6, H2O.7 ZN.5: 3 residues within 4Å: Chain A: H.76 Ligands: CL.8, CL.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76 ZN.6: 3 residues within 4Å: Chain A: C.114, H.275 Ligands: CL.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.114, A:H.275, H2O.5

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

CL.7: 6 residues within 4Å: Chain A: T.13, V.14, D.15, N.18, H.20, E.70 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.5, CL.9 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.5, CL.8 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: N.112, N.113, C.114, H.275 Ligands: ZN.6 Ligand excluded by PLIP

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

ACT.11: 2 residues within 4Å: Chain A: Q.177, H.178 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.178

5 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.12: 3 residues within 4Å: Chain A: H.258 Ligands: UNX.13, UNX.15 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain A: H.258 Ligands: UNX.12 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Ligands: UNX.15, UNX.16 No protein-ligand interaction detected (PLIP) UNX.15: 2 residues within 4Å: Ligands: UNX.12, UNX.14 No protein-ligand interaction detected (PLIP) UNX.16: 1 residues within 4Å: Ligands: UNX.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder441. to be published

Release Date

2020-08-12

Peptides

Papain-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease

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