SMTL ID : 8e61.1

Crystal structure of SARS-CoV-2 3CL protease in complex with a m-chlorophenyl dimethyl sulfane inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: R.8, K.9 Chain B: K.9 Ligand excluded by PLIP

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

VLU.2: 19 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, L.171, P.172, H.176, D.191, R.192, Q.193, T.194, Q.196 Ligands: VM0.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.45, A:M.169 Hydrogen bonds: A:F.144, A:S.148, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 VLU.4: 14 residues within 4Å: Chain B: 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 Ligands: VM0.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:F.144, B:S.148, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193 Water bridges: B:G.147

2 x VM0: (1S,2S)-2-{[N-({2-[(3-chlorophenyl)sulfanyl]-2-methylpropoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

VM0.3: 20 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, L.171, P.172, H.176, D.191, R.192, Q.193, T.194, Q.196 Ligands: VLU.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:M.169 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 VM0.5: 16 residues within 4Å: Chain B: 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, R.192, Q.193 Ligands: VLU.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Q.193 Hydrogen bonds: B:F.144, B:G.147, B:S.148, B:S.148, B:C.149, B:H.168, B:E.170, B:E.170, B:Q.193, B:Q.193

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

2022-09-07

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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