SMTL ID : 7dgi.1

The co-crystal structure of SARS-CoV-2 main protease with peptidomimetic inhibitor N-((S)-3-methyl-1-(((S)-4-methyl-1-oxo-1-(((S)-1-oxo-3-((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)pentan-2-yl)amino)-1-oxobutan-2-yl)-4-nitrobenzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x H6L: ~{N}-[(2~{S})-3-methyl-1-[[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]pentan-2-yl]amino]-1-oxidanylidene-butan-2-yl]-4-nitro-benzamide(Covalent)

H6L.1: 20 residues within 4Å: Chain A: H.41, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, P.168, H.172, D.187, Q.189, T.190, A.191, Q.192, A.193 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.41, A:M.165, A:Q.189, A:Q.192 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:Q.189, A:Q.192, B:S.1 H6L.2: 22 residues within 4Å: Chain A: S.1 Chain B: H.41, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, F.185, D.187, Q.189, T.190, A.191, Q.192 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.41, B:M.165, B:L.167, B:P.168 Hydrogen bonds: B:G.143, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166, B:Q.189, A:S.1, A:S.1 Water bridges: B:H.41, B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., The structure-based design of peptidomimetic inhibitors against SARS-CoV-2 3C like protease as Potent anti-viral drug candidate. Eur.J.Med.Chem. (2022)

Release Date

2021-11-24

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

Related Entries With Identical Sequence