SMTL ID : 8doy.1

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-198

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 4 residues within 4Å: Chain A: E.167, P.169, Q.190 Ligands: T1X.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.169

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 7 residues within 4Å: Chain A: R.106, F.135, N.181, F.182, G.184, P.185 Ligands: DMS.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.106, A:G.184

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

DMS.3: 6 residues within 4Å: Chain A: N.85, C.86, G.180, N.181, F.182 Ligands: MES.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.182 DMS.6: 3 residues within 4Å: Chain B: S.63, N.64, H.65 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.64 Water bridges: B:N.64

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.4: 5 residues within 4Å: Chain A: R.5, K.6 Chain B: K.6, Y.127, Q.128 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.128, A:R.5, A:K.6

2 x T1X: 7-fluoro-N-[(2S)-1-({(1S,2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide(Covalent)

T1X.5: 22 residues within 4Å: Chain A: T.26, H.42, M.50, F.141, L.142, 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, A.192 Ligands: 1PE.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.26, A:D.188, A:A.192 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:Q.190 T1X.7: 19 residues within 4Å: Chain B: T.26, L.28, H.42, 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, Q.190, T.191, A.192 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.26, B:A.192 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:Q.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsuji, K. et al., Potent and biostable inhibitors of the main protease of SARS-CoV-2. Iscience (2022)

Release Date

2022-08-24

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5