SMTL ID : 9cdm.1

SARS-CoV-2 Mpro L50F mutant in complex with small molecule inhibitor Mpro61

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x XEK: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione(Non-covalent)

XEK.1: 24 residues within 4Å: Chain A: T.25, T.26, L.27, 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, T.190, Q.192 Chain B: S.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:M.165, A:L.167, A:P.168, A:Q.192 Hydrogen bonds: A:T.26, A:T.26, A:G.143, A:C.145, A:E.166 pi-Stacking: A:H.41 Halogen bonds: A:Q.189 XEK.3: 24 residues within 4Å: Chain A: S.1 Chain B: T.25, T.26, L.27, 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, T.190, Q.192 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:M.165, B:L.167, B:P.168, B:Q.192 Hydrogen bonds: B:T.26, B:T.26, B:G.143, B:C.145, B:E.166 pi-Stacking: B:H.41 Halogen bonds: B:Q.189

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 3 residues within 4Å: Chain A: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP) DMS.4: 3 residues within 4Å: Chain B: Q.74, L.75, R.76 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kenneson, J.R. et al., Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (Mpro) with Noncovalent Preclinical Candidate, Mpro61. Acs Bio Med Chem Au (2025)

Release Date

2025-02-05

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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