SMTL ID : 8dpr.1

Crystal structure of SARS-CoV-2 main protease in complex with inhibitor TKB-248

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x T43: 2,2,2-trifluoro-N-{(2S)-1-[(1R,2S,5S)-2-({(2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamothioyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-3-yl]-3,3-dimethyl-1-oxobutan-2-yl}acetamide(Covalent)

T43.1: 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 15 PLIP interactions: 15 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:S.145, A:C.146, A:H.165, A:E.167, A:E.167, A:E.167, A:T.191 Halogen bonds: A:Q.193 T43.4: 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:S.145, B:C.146, B:H.165, B:E.167, B:E.167, B:T.191 Halogen bonds: B:Q.193

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

DMS.2: 4 residues within 4Å: Chain A: R.223, F.224, T.225, D.264 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.264 DMS.5: 4 residues within 4Å: Chain B: R.223, F.224, T.225, D.264 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.264

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: N.204, V.205, W.208, E.289, D.290, E.291, F.292 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.204, A:E.289 ZN.6: 7 residues within 4Å: Chain B: N.204, V.205, W.208, E.289, D.290, E.291, F.292 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:N.204, B:E.289

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

2022-08-24

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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