SMTL ID : 8vqx.1

Structure of SARS-CoV-2 main protease with potent peptide aldehyde inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x 01: N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-1-(1H-indole-2-carbonyl)-4,4-dimethyl-L-prolinamide

01.1: 18 residues within 4Å: Chain A: H.50, F.149, L.150, N.151, G.152, S.153, C.154, H.172, H.173, M.174, E.175, P.177, H.181, D.196, R.197, Q.198, T.199, A.200 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.177, A:A.200 Hydrogen bonds: A:F.149, A:G.152, A:S.153, A:S.153, A:C.154, A:H.173, A:E.175 01.6: 18 residues within 4Å: Chain B: H.50, F.149, L.150, N.151, G.152, S.153, C.154, H.172, H.173, M.174, E.175, P.177, H.181, D.196, R.197, Q.198, T.199, A.200 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.177, B:A.200 Hydrogen bonds: B:F.149, B:G.152, B:S.153, B:S.153, B:C.154, B:H.173, B:E.175, B:E.175

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: N.230, F.232, D.272, A.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.230, A:F.232, A:D.272, A:D.272 NA.7: 4 residues within 4Å: Chain B: N.230, F.232, D.272, A.275 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.230, B:N.230, B:F.232

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

EDO.3: 9 residues within 4Å: Chain A: M.26, V.27, Q.28, Q.78, A.79, G.80, N.128, G.129, S.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.26, A:G.80 Water bridges: A:N.128 EDO.4: 7 residues within 4Å: Chain A: M.15, A.16, F.17, Q.136, R.307 Chain B: S.132, G.133 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.136, A:R.307, B:S.132 Water bridges: A:M.15, A:M.15 EDO.8: 9 residues within 4Å: Chain B: M.26, V.27, Q.28, Q.78, A.79, G.80, N.128, G.129, S.130 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.26, B:G.80 Water bridges: B:N.128 EDO.9: 7 residues within 4Å: Chain A: S.132, G.133 Chain B: M.15, A.16, F.17, Q.136, R.307 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.132, B:Q.136, B:R.307 Water bridges: B:M.15, B:M.15

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 13 residues within 4Å: Chain A: K.14, M.15, A.16, V.134, Y.135, Q.136 Chain B: K.14, M.15, A.16, V.134, Y.135, Q.136 Ligands: PEG.10 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.16, B:Q.136, B:Q.136, A:Q.136, A:Q.136 PEG.10: 13 residues within 4Å: Chain A: K.14, M.15, A.16, V.134, Y.135, Q.136 Chain B: K.14, M.15, A.16, V.134, Y.135, Q.136 Ligands: PEG.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.16, A:Q.136, A:Q.136, B:Q.136, B:Q.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carney, D.W. et al., Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity. Bioorg.Med.Chem. (2024)

Release Date

2024-08-07

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5