SMTL ID : 8e63.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x UV2: (1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-[(N-{[2-(phenylsulfanyl)ethoxy]carbonyl}-L-leucyl)amino]propane-1-sulfonic acid(Covalent)

UV2.1: 18 residues within 4Å: Chain A: H.45, M.53, F.144, L.145, N.146, S.148, C.149, H.167, H.168, M.169, E.170, P.172, H.176, D.191, Q.193, T.194, A.195 Ligands: UUR.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.45, A:P.172, A:D.191, A:A.195 Hydrogen bonds: A:F.144, A:H.168, A:E.170, A:Q.193, A:Q.193 Water bridges: A:G.147 UV2.3: 15 residues within 4Å: Chain B: H.45, F.144, N.146, S.148, C.149, H.167, H.168, M.169, E.170, H.176, D.191, R.192, Q.193, T.194 Ligands: UUR.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.45 Hydrogen bonds: B:F.144, B:H.168, B:E.170, B:E.170, B:Q.193 Water bridges: B:G.147, B:Q.193, B:Q.193

2 x UUR: 2-phenylsulfanylethyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate(Covalent)

UUR.2: 20 residues within 4Å: Chain A: H.45, M.53, F.144, L.145, N.146, G.147, S.148, C.149, H.167, H.168, M.169, E.170, P.172, H.176, D.191, R.192, Q.193, T.194, A.195 Ligands: UV2.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.191, A:A.195 Hydrogen bonds: A:F.144, A:G.147, A:S.148, A:S.148, A:C.149, A:H.168, A:E.170, A:Q.193, A:Q.193 UUR.4: 15 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, Q.193 Ligands: UV2.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.45, B:D.191 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, B:Q.193

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

PG4.5: 4 residues within 4Å: Chain B: A.259, Q.260, T.261, G.262 No protein-ligand interaction detected (PLIP)

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

2022-09-28

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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