SMTL ID : 8dox.1

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-245

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

2 x T2L: (1R,2S,5S)-N-{(1S,2S)-1-(4-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)

T2L.1: 21 residues within 4Å: Chain A: T.26, H.42, C.45, M.50, F.141, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, L.168, P.169, H.173, D.188, R.189, Q.190, T.191, Q.193 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.26, A:H.42, A:M.166, A:E.167 Hydrogen bonds: A:F.141, A:G.144, A:S.145, A:C.146, A:H.165, A:E.167, A:E.167, A:T.191 Halogen bonds: A:Q.193 T2L.3: 21 residues within 4Å: Chain B: T.26, H.42, C.45, M.50, F.141, N.143, G.144, S.145, C.146, H.164, H.165, M.166, E.167, L.168, P.169, H.173, D.188, R.189, Q.190, T.191, Q.193 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.26, B:H.42, B:M.166, B:E.167 Hydrogen bonds: B:F.141, B:G.144, B:S.145, B:C.146, B:H.165, B:E.167, B:E.167, B:E.167, B:T.191 Halogen bonds: B:Q.193

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

DMS.2: 3 residues within 4Å: Chain A: Q.75, L.76, R.77 No protein-ligand interaction detected (PLIP) DMS.4: 3 residues within 4Å: Chain B: Q.75, L.76, R.77 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Higashi-Kuwata, N. et al., Identification of SARS-CoV-2 M pro inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2. Nat Commun (2023)

Release Date

2022-09-21

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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