SMTL ID : 9mvp.1

Crystal Structure of SARS-CoV-2 Main Protease (Mpro)in Complex with Inhibitor AVI-4516

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x 01: (3M,5P)-5-(1H-1,2,3-benzotriazol-1-yl)-3-(isoquinolin-4-yl)-6-methyl-1-(prop-2-en-1-yl)pyrimidine-2,4(1H,3H)-dione

01.1: 17 residues within 4Å: Chain A: T.26, L.27, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188, Q.189 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.27, A:N.142, A:M.165, A:E.166 Hydrogen bonds: A:G.143, A:S.144, A:E.166 01.3: 17 residues within 4Å: Chain B: T.26, L.27, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, D.187, R.188, Q.189 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.27, B:N.142, B:M.165, B:E.166 Hydrogen bonds: B:G.143, B:S.144, B:E.166

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

EDO.2: 1 residues within 4Å: Chain A: H.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.80 EDO.4: 1 residues within 4Å: Chain B: H.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Detomasi, T.C. et al., Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus M Pro inhibitors with potent in vivo efficacy. Sci Adv (2025)

Release Date

2025-07-23

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

Related Entries With Identical Sequence