SMTL ID : 8uh9.1

Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-272

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x WOK: (1R,2S,5S)-N-{(1S,2S)-1-(5-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide(Covalent)

WOK.1: 25 residues within 4Å: Chain A: T.25, H.41, C.44, S.46, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 Chain B: S.1 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.25, A:H.41, A:M.165, A:V.166, A:D.187 Hydrogen bonds: A:G.143, A:C.145, A:H.164, A:V.166, A:V.166, A:H.172, A:T.190, B:S.1, B:S.1 Halogen bonds: A:S.46 WOK.3: 25 residues within 4Å: Chain A: S.1 Chain B: T.25, H.41, C.44, S.46, M.49, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, V.166, L.167, P.168, H.172, D.187, R.188, Q.189, T.190, Q.192 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.25, B:H.41, B:M.165, B:V.166, B:D.187 Hydrogen bonds: B:G.143, B:C.145, B:H.164, B:V.166, B:V.166, B:T.190, A:S.1, A:S.1 Halogen bonds: B:S.46

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: I.78, G.79, H.80, S.81, K.88, K.90 No protein-ligand interaction detected (PLIP) PEG.4: 6 residues within 4Å: Chain B: I.78, G.79, H.80, S.81, K.88, K.90 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Higashi-Kuwata, N. et al., TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir. To Be Published

Release Date

2023-12-20

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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