SMTL ID : 9cjv.1

X-ray crystal structure of SARS-CoV-2 main protease complex with Bofutrelvir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x FHR: ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide(Covalent)

FHR.1: 23 residues within 4Å: Chain A: H.41, C.44, M.49, P.52, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189 Chain B: S.1 Ligands: DMS.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.189 Hydrogen bonds: A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, B:S.1 Water bridges: A:N.142 pi-Stacking: A:H.41 FHR.4: 23 residues within 4Å: Chain A: S.1 Chain B: H.41, C.44, M.49, P.52, Y.54, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, H.172, D.187, R.188, Q.189 Ligands: DMS.5 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.189 Hydrogen bonds: B:G.143, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, A:S.1 Water bridges: B:N.142 pi-Stacking: B:H.41

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

DMS.2: 6 residues within 4Å: Chain A: T.25, L.27, H.41, V.42, C.44 Ligands: FHR.1 No protein-ligand interaction detected (PLIP) DMS.3: 7 residues within 4Å: Chain A: G.2, F.3, R.4, L.282, G.283 Chain B: K.137, G.138 No protein-ligand interaction detected (PLIP) DMS.5: 6 residues within 4Å: Chain B: T.25, L.27, H.41, V.42, C.44 Ligands: FHR.4 No protein-ligand interaction detected (PLIP) DMS.6: 7 residues within 4Å: Chain A: K.137, G.138 Chain B: G.2, F.3, R.4, L.282, G.283 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esler, M.A. et al., X-ray crystal structure of SARS-CoV-2 main protease complex with Bofutrelvir. To Be Published

Release Date

2025-07-09

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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