SMTL ID : 8dz1.1

Crystal Structure of SARS-CoV-2 Main protease mutant M49I in complex with Ensitrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 3 residues within 4Å: Chain A: Y.37, Y.101, F.103 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.103 DMS.2: 1 residues within 4Å: Chain A: R.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:R.40 DMS.4: 3 residues within 4Å: Chain B: R.40, P.52, Y.54 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.54

2 x 7YY: 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione(Non-covalent)

7YY.3: 19 residues within 4Å: Chain A: T.24, T.25, T.26, H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, H.172, D.187, R.188, Q.189 Chain B: S.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.25 Hydrogen bonds: A:T.26, A:G.143, A:S.144, A:S.144, A:C.145, A:E.166 Salt bridges: A:E.166 pi-Cation interactions: A:H.41 Halogen bonds: A:C.145, A:Q.189 7YY.5: 19 residues within 4Å: Chain A: S.1 Chain B: T.24, T.25, T.26, L.27, H.41, I.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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.49 Hydrogen bonds: B:T.26, B:N.142, B:G.143, B:S.144, B:S.144, B:C.145, B:E.166 Salt bridges: B:E.166 pi-Stacking: B:H.41 pi-Cation interactions: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noske, G.D. et al., Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease. J.Biol.Chem. (2023)

Release Date

2022-10-05

Peptides

Replicase polyprotein 1ab: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Replicase polyprotein 1ab

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