SMTL ID : 8e68.1

Crystal structure of SARS-CoV-2 3CL protease in complex with a p-fluorodimethyl oxybenzene inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x WGO: N~2~-{[2-(4-fluorophenoxy)-2-methylpropoxy]carbonyl}-N-{(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide(Covalent)

WGO.1: 16 residues within 4Å: Chain A: H.45, F.144, L.145, N.146, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, Q.193, T.194, A.195 Ligands: WGU.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.45, A:A.195 Hydrogen bonds: A:H.168, A:E.170, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:G.147, A:G.147 WGO.3: 17 residues within 4Å: Chain B: H.45, M.53, Y.58, F.144, L.145, N.146, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, R.192, Q.193 Ligands: WGU.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:S.148, B:H.168, B:E.170, B:E.170, B:Q.193 Water bridges: B:G.147

2 x WGU: (1S,2S)-2-[(N-{[2-(4-fluorophenoxy)-2-methylpropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

WGU.2: 17 residues within 4Å: Chain A: H.45, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, Q.193, T.194, A.195 Ligands: WGO.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:A.195 Hydrogen bonds: A:F.144, A:G.147, A:S.148, A:C.149, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 WGU.4: 18 residues within 4Å: Chain B: H.45, M.53, Y.58, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, R.192, Q.193 Ligands: WGO.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:G.147, B:C.149, B:H.168, B:E.170, B:E.170, B:E.170, B:Q.193

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 8 residues within 4Å: Chain B: E.18, G.19, M.21, W.35, A.74, V.77, L.79, N.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.21 Water bridges: B:G.75, B:Q.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dampalla, C.S. et al., Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur.J.Med.Chem. (2023)

Release Date

2022-09-14

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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