SMTL ID : 9f39.1

Crystal structure of SARS-CoV-2 Mpro in complex with RK-54

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x 01: (2R,3R)-3-[[(2S)-3-cyclopropyl-2-[3-(2-methylpropanoylamino)-2-oxidanylidene-pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide

01.1: 18 residues within 4Å: Chain A: T.26, 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, T.190 Chain B: S.1 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:S.1, A:F.140, A:N.142, A:G.143, A:S.144, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166 Hydrophobic interactions: A:H.41, A:D.187, A:Q.189, A:Q.189 01.2: 18 residues within 4Å: Chain A: S.1 Chain B: T.26, 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, T.190 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.41, B:D.187, B:Q.189, B:Q.189 Hydrogen bonds: B:F.140, B:N.142, B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akula, R.K. et al., Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease. J.Med.Chem. (2025)

Release Date

2025-01-29

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase nsp5

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