SMTL ID : 7l8h.1

EV68 3C protease (3Cpro) in Complex with Rupintrivir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x AG7: 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER(Covalent)

AG7.1: 22 residues within 4Å: Chain A: K.28, F.31, H.46, E.77, Y.128, L.131, N.132, L.133, G.134, T.136, T.148, R.149, A.150, G.151, C.153, H.167, V.168, G.169, G.170, N.171, G.172, F.176 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.31, A:H.46, A:L.133, A:L.133 Hydrogen bonds: A:G.134, A:T.148, A:T.148, A:H.167, A:V.168, A:G.170, A:G.170, A:N.171 Water bridges: A:T.148 pi-Stacking: A:H.46 AG7.2: 24 residues within 4Å: Chain B: K.28, F.31, H.46, A.47, N.75, E.77, L.131, N.132, L.133, G.134, T.136, T.148, R.149, A.150, G.151, Q.152, C.153, H.167, V.168, G.169, G.170, N.171, G.172, F.176 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:K.28, B:H.46, B:L.131, B:L.133 Hydrogen bonds: B:G.134, B:T.148, B:T.148, B:H.167, B:V.168, B:G.170, B:G.170, B:N.171 Water bridges: B:T.148 Salt bridges: B:H.46 pi-Stacking: B:H.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lockbaum, G.J. et al., Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode. Biochemistry (2021)

Release Date

2021-09-22

Peptides

3C Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C Protease