SMTL ID : 6w81.1

Structure of PEDV main protease bound to potent broad-spectrum non-covalent inhibitor X77

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x X77: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide(Non-covalent)

X77.1: 22 residues within 4Å: Chain A: M.25, A.26, L.27, H.41, A.44, T.47, I.51, Y.53, F.139, I.140, N.141, G.142, C.144, H.162, Q.163, L.164, E.165, H.171, D.186, Q.187, P.188 Chain B: A.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.41, A:E.165, A:P.188 Hydrogen bonds: A:H.41, A:N.141, A:G.142, A:E.165 X77.2: 21 residues within 4Å: Chain A: A.1 Chain B: A.26, L.27, H.41, S.46, T.47, Y.53, F.139, I.140, N.141, G.142, C.144, H.162, Q.163, L.164, E.165, H.171, D.186, Q.187, P.188, T.189 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.41, B:L.164, B:E.165, B:P.188 Hydrogen bonds: B:H.41, B:G.142, B:E.165 Water bridges: B:A.26, B:N.141, B:N.141

1 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 8 residues within 4Å: Chain A: R.4, R.136 Chain B: R.4, K.5, R.136, Y.280, E.286, F.287 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:K.5, B:Y.280 Hydrogen bonds: B:K.5, B:K.5, B:E.286 Water bridges: B:R.4, B:R.4, B:R.136, B:R.136, A:R.4, A:R.4, A:K.5 Salt bridges: B:R.4, B:R.136, A:R.4, A:R.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mesecar, A.D., A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19). To Be Published

Release Date

2021-03-24

Peptides

Peptidase C30: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptidase C30