SMTL ID : 8aj0.1

Mpro of SARS COV-2 in complex with the RK-90 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

2 x MJ0: (2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(3-phenylpropanoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide(Covalent)

MJ0.1: 21 residues within 4Å: Chain A: 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, T.190, A.191 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.165, A:P.168, A:D.187, A:Q.189, A:A.191 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, B:S.1 Water bridges: A:N.142 MJ0.4: 20 residues within 4Å: Chain A: S.1 Chain B: T.26, H.41, 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, A.191 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.142, B:M.165, B:P.168, B:D.187, B:Q.189, B:A.191 Hydrogen bonds: B:G.143, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 7 residues within 4Å: Chain A: S.284, A.285, L.286 Chain B: S.284, A.285, L.286 Ligands: NA.3 Ligand excluded by PLIP

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

NA.3: 4 residues within 4Å: Chain A: S.284, E.288 Chain B: S.284 Ligands: CL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.288

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

2023-08-16

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

3C-like proteinase nsp5

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