SMTL ID : 7skr.1

BtSCoV-Rf1.2004 Papain-Like protease bound to the non-covalent inhibitor 37

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-dimer

Ligands

2 x 9OZ: N-[(2-methoxypyridin-4-yl)methyl]-2-[(1R)-1-(naphthalen-1-yl)ethyl]-2-azaspiro[3.3]heptane-6-carboxamide(Non-covalent)

9OZ.1: 10 residues within 4Å: Chain A: L.166, G.167, D.168, P.252, Y.268, N.271, Y.272, Q.273, Y.277, T.305 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.252, A:Y.268, A:Y.268, A:Y.272, A:T.305 Hydrogen bonds: A:Y.272, A:Q.273, A:Y.277 Salt bridges: A:D.168 pi-Stacking: A:Y.272, A:Y.272 9OZ.5: 10 residues within 4Å: Chain B: L.166, G.167, D.168, P.252, Y.268, N.271, Y.272, Q.273, Y.277, T.305 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.252, B:Y.268, B:Y.268, B:Y.272, B:T.305 Hydrogen bonds: B:Y.272, B:Q.273 Salt bridges: B:D.168 pi-Stacking: B:Y.272, B:Y.272

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 2 residues within 4Å: Chain A: Y.211, M.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.212 DMS.6: 2 residues within 4Å: Chain B: Y.211, M.212 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.212

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.193, C.196, C.228, C.230 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.193, A:C.196, A:C.228, A:C.230 ZN.4: 3 residues within 4Å: Chain A: N.113, N.114, C.115 No protein-ligand interaction detected (PLIP) ZN.7: 4 residues within 4Å: Chain B: C.193, C.196, C.228, C.230 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.193, B:C.196, B:C.228, B:C.230 ZN.8: 3 residues within 4Å: Chain B: N.113, N.114, C.115 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freitas, B.T. et al., Exploring Noncovalent Protease Inhibitors for the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses. Acs Infect Dis. (2022)

Release Date

2022-03-02

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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