SMTL ID : 8eua.1

Structure of SARS-CoV2 PLpro bound to a covalent inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

1 x WUK: methyl 4-{2-[3-(2-{[(1R)-1-(naphthalen-1-yl)ethyl]carbamoyl}phenyl)propanoyl]hydrazinyl}-4-oxobutanoate(Covalent)

WUK.1: 18 residues within 4Å: Chain A: W.108, N.111, N.112, C.113, Y.114, L.164, G.165, D.166, E.169, P.249, P.250, Y.266, Y.270, Q.271, C.272, G.273, H.274, Y.275 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.164, A:L.164, A:D.166, A:P.249, A:P.250, A:Y.266, A:Y.266, A:Y.270, A:Q.271 Hydrogen bonds: A:N.111, A:C.113, A:G.165, A:G.165, A:D.166, A:Q.271, A:G.273, A:G.273, A:Y.275 Salt bridges: A:H.274 pi-Stacking: A:Y.270, A:Y.270

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.191, C.194, C.226, C.228 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.191, A:C.194, A:C.226, A:C.228 ZN.3: 1 residues within 4Å: Chain A: C.272 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.272 ZN.4: 1 residues within 4Å: Chain A: H.75 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.75

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: Y.138, R.142 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanders, B.C. et al., Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nat Commun (2023)

Release Date

2023-04-05

Peptides

Papain-like protease nsp3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease nsp3