SMTL ID : 9h0f.1

SARS-CoV-2 Mpro in complex with a silicon-containing inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: L.141, N.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.142

2 x 01: methyl-N-[(2S)-1-[(5R)-5-[[(2S)-1-azanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]-3,3-dimethyl-1,3-azasilolidin-1-yl]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]carbamate

01.2: 19 residues within 4Å: Chain A: H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, H.172, D.187, R.188, Q.189, T.190, Q.192 Ligands: CL.13 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.140, A:G.143, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:T.190 Water bridges: B:S.1 01.15: 19 residues within 4Å: Chain B: H.41, M.49, 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, T.190, Q.192 Ligands: DMS.14 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166, B:E.166

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain A: E.14, G.15, M.17, V.18, W.31, A.70, G.71, K.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.15, A:M.17 SO4.4: 3 residues within 4Å: Chain A: G.2, F.3, L.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.3 SO4.5: 5 residues within 4Å: Chain A: V.212, I.213, R.217, Q.256, T.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.256 Salt bridges: A:R.217 SO4.6: 6 residues within 4Å: Chain A: M.6, F.8, Q.127, D.295, R.298 Chain B: S.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.6, A:Q.127 Water bridges: A:M.6 Salt bridges: A:R.298 SO4.16: 8 residues within 4Å: Chain B: C.22, G.23, T.24, T.25, V.42, I.43, C.44, T.45 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.24, B:T.25, B:T.25, B:T.25 Water bridges: B:S.46 SO4.17: 10 residues within 4Å: Chain B: M.17, V.18, Q.19, Q.69, A.70, G.71, N.119, G.120, S.121 Ligands: SO4.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.71, B:G.71, B:N.119 SO4.18: 4 residues within 4Å: Chain B: F.223, A.266, K.269, E.270 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.273, B:Q.273 Salt bridges: B:K.269 SO4.19: 4 residues within 4Å: Chain B: I.249, P.252, P.293, V.297 1 PLIP interactions: 1 interactions with chain B Water bridges: B:I.249 SO4.20: 9 residues within 4Å: Chain B: E.14, G.15, C.16, M.17, W.31, A.70, G.71, K.97 Ligands: SO4.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.17, B:G.71 Water bridges: B:G.15, B:N.95 Salt bridges: B:K.97 SO4.21: 3 residues within 4Å: Chain B: Q.244, D.245, D.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.245, B:D.245 Water bridges: B:D.248 SO4.22: 3 residues within 4Å: Chain B: G.251, P.252, A.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.251 SO4.23: 2 residues within 4Å: Chain B: N.274, N.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.274 Water bridges: B:R.279, B:R.279, B:R.279 SO4.24: 5 residues within 4Å: Chain A: Y.118, S.123 Chain B: M.6, R.298, Q.299 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.298, A:S.123 Salt bridges: B:R.298 Water bridges: A:Y.118, A:Y.118 SO4.25: 2 residues within 4Å: Chain B: F.223, T.224 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.224

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: I.249, V.297 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: P.293 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: P.52, N.53, Y.54 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: K.5, Q.127 Chain B: K.5 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: N.221, R.222 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: M.82 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: G.143 Ligands: 01.2 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: M.6, R.298 Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

DMS.14: 4 residues within 4Å: Chain B: T.26, N.142, G.143 Ligands: 01.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.143 Water bridges: B:T.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laczi, D. et al., Silaproline-bearing nirmatrelvir derivatives are potent inhibitors of the SARS-CoV-2 main protease highlighting the value of silicon-derivatives in structure-activity-relationship studies. Eur J Med Chem (2025)

Release Date

2025-06-11

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase nsp5

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