SMTL ID : 9f3a.1

Crystal structure of SARS-CoV-2 Mpro in complex with RK-325

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x 01: tert-butyl N-[1-[(2S)-3-cyclopropyl-1-[[(2S,3R)-4-(methylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-5-fluoranyl-2-oxidanylidene-pyridin-3-yl]carbamate

01.1: 20 residues within 4Å: Chain A: T.26, H.41, M.49, 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, D.187, R.188, Q.189 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.41, A:D.187 Hydrogen bonds: A:N.142, A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, B:S.1, B:S.1 Halogen bonds: A:Q.189 01.2: 20 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, L.167, P.168, H.172, D.187, R.188, Q.189 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.165, B:D.187, B:Q.189 Hydrogen bonds: B:N.142, B:G.143, 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
B

3C-like proteinase nsp5

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