SMTL ID : 9cju.1

Structure of SARS-CoV-2 main protease in complex with Bofutrelvir in orthorhombic form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 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, 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: EDO.2, EDO.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.41, A:Q.189 Hydrogen bonds: A:F.140, A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166, A:Q.189 pi-Stacking: A:H.41 FHR.8: 23 residues within 4Å: Chain A: S.1 Chain B: H.41, C.44, M.49, 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: EDO.9, EDO.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.41 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 Water bridges: B:Q.189 pi-Stacking: B:H.41

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 1 residues within 4Å: Ligands: FHR.1 No protein-ligand interaction detected (PLIP) EDO.3: 5 residues within 4Å: Chain A: Y.118, L.141, N.142 Chain B: S.301, G.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.142 EDO.4: 7 residues within 4Å: Chain A: K.5, M.6, A.7, Y.126, Q.127 Chain B: R.4, K.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.4, A:K.5, A:Q.127 Water bridges: B:R.4, B:Q.127 EDO.6: 7 residues within 4Å: Chain A: P.168, R.188, Q.189, T.190, A.191, Q.192 Ligands: FHR.1 No protein-ligand interaction detected (PLIP) EDO.9: 2 residues within 4Å: Chain B: N.142 Ligands: FHR.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.142 EDO.10: 9 residues within 4Å: Chain B: M.165, E.166, L.167, P.168, R.188, Q.189, T.190, Q.192 Ligands: FHR.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.166, B:Q.189, B:T.190, B:Q.192

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 8 residues within 4Å: Chain A: E.14, G.15, C.16, M.17, V.18, W.31, A.70, K.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.15, A:K.97 Water bridges: A:E.14, A:G.15 PEG.7: 6 residues within 4Å: Chain A: R.298, S.301 Chain B: Y.118, S.123, L.141, N.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.123, B:S.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esler, M.A., To be published. To Be Published

Release Date

2025-07-09

Peptides

Non-structural protein 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Non-structural protein 7

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