SMTL ID : 8e6a.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: S.288, A.289 Chain B: S.288, A.289 Ligand excluded by PLIP

2 x WIX: (1S,2S)-2-[(N-{[(2R)-2-(3-chlorophenyl)-2-hydroxypropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

WIX.2: 20 residues within 4Å: Chain A: 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, T.194, Q.196 Ligands: WJ0.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.45, A:D.191 Hydrogen bonds: A:F.144, A:G.147, A:C.149, A:H.168, A:E.170, A:E.170, A:Q.193 Halogen bonds: A:Q.196 WIX.4: 21 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, L.171, H.176, D.191, R.192, Q.193, T.194, Q.196 Ligands: WJ0.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.45, B:Q.193 Hydrogen bonds: B:F.144, B:G.147, B:S.148, B:C.149, B:H.168, B:E.170, B:E.170, B:Q.193 Halogen bonds: B:Q.196

2 x WJ0: (1R,2S)-2-[(N-{[(2S)-2-(3-chlorophenyl)-2-hydroxypropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propane-1-sulfonic acid(Covalent)

WJ0.3: 18 residues within 4Å: Chain A: H.45, M.53, Y.58, F.144, L.145, N.146, C.149, H.167, H.168, M.169, E.170, H.176, D.191, R.192, Q.193, T.194, Q.196 Ligands: WIX.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.45, A:D.191, A:Q.193 Hydrogen bonds: A:H.168, A:E.170, A:E.170, A:Q.193 Halogen bonds: A:Q.196 WJ0.5: 20 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, L.171, H.176, D.191, R.192, Q.193, T.194, Q.196 Ligands: WIX.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:H.45, B:Q.193 Hydrogen bonds: B:H.168, B:E.170, B:E.170, B:Q.193 Halogen bonds: B:Q.196

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

2022-09-21

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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