SMTL ID : 7skq.1

BtSCoV-Rf1.2004 Papain-Like protease bound to the non-covalent inhibitor GRL-0617

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.16 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.2: 5 residues within 4Å: Chain A: H.93, W.97, D.112 Chain B: Q.273, C.274 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.93, A:D.112, A:D.112, B:C.274 ZN.5: 5 residues within 4Å: Chain B: C.193, C.196, C.228, C.230, R.232 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.193, B:C.196, B:C.228, B:C.230 ZN.6: 4 residues within 4Å: Chain A: Q.273, C.274 Chain B: H.93, D.112 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.93, B:D.112, B:D.112, A:C.274

2 x TTT: 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide(Non-covalent)

TTT.3: 10 residues within 4Å: Chain A: L.166, G.167, D.168, E.171, P.252, Y.268, Y.272, Q.273, Y.277, T.305 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.166, A:P.252, A:Y.268, A:Y.268, A:Y.272, A:T.305 Hydrogen bonds: A:D.168, A:Y.272, A:Q.273, A:Q.273, A:Y.277 pi-Stacking: A:Y.272, A:Y.272 TTT.4: 9 residues within 4Å: Chain B: L.166, G.167, D.168, P.252, Y.268, Y.272, Q.273, Y.277, T.305 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.166, B:D.168, B:P.252, B:Y.268, B:Y.268, B:Y.272, B:T.305 Hydrogen bonds: B:D.168, B:D.168, B:Q.273 pi-Stacking: B:Y.272

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
B

3C-like proteinase

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