SMTL ID : 8uld.1

SARA CoV-2 3C-like protease in complex with GSK3487016A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x WYR: N-[(benzyloxy)carbonyl]-4-fluoro-L-phenylalanyl-N-{(2S,3R)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]-4-[(propan-2-yl)amino]butan-2-yl}-L-leucinamide(Covalent)

WYR.1: 19 residues within 4Å: Chain A: T.45, T.46, H.61, F.160, N.162, G.163, S.164, C.165, H.183, H.184, M.185, E.186, P.188, H.192, D.207, Q.209, T.210, A.211, Q.212 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.45, A:N.162, A:M.185, A:P.188 Hydrogen bonds: A:G.163, A:S.164, A:C.165, A:H.184, A:E.186, A:E.186, A:E.186, A:Q.209 WYR.4: 19 residues within 4Å: Chain B: T.45, T.46, H.61, F.160, N.162, G.163, S.164, C.165, H.183, H.184, M.185, E.186, P.188, H.192, D.207, Q.209, T.210, A.211, Q.212 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.45, B:N.162, B:M.185, B:P.188 Hydrogen bonds: B:G.163, B:S.164, B:C.165, B:H.184, B:E.186, B:E.186, B:E.186, B:Q.209

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: D.236, W.238, R.299, T.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.236, A:R.299, A:R.299 EDO.3: 6 residues within 4Å: Chain A: R.24, K.25 Chain B: K.25, Y.146, Q.147 Ligands: EDO.6 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.27, B:Q.147, A:R.24, A:K.25 EDO.5: 4 residues within 4Å: Chain B: D.236, W.238, R.299, T.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.236, B:R.299, B:R.299 EDO.6: 6 residues within 4Å: Chain A: K.25, Y.146, Q.147 Chain B: R.24, K.25 Ligands: EDO.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.27, A:Q.147, B:R.24, B:K.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barton, L.S. et al., Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement. Bioorg.Med.Chem. (2024)

Release Date

2024-02-14

Peptides

Replicase polyprotein 1a: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Replicase polyprotein 1a