SMTL ID : 8e5x.1

Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl sulfinyl benzene inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x UO9: (2~{S})-2-[[(2~{S})-4-methyl-2-[[2-methyl-2-[oxidanyl(phenyl)-$l^{3}-sulfanyl]propoxy]carbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

UO9.1: 18 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, Q.193, T.194, A.195 Ligands: URR.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.45, A:A.195 Hydrogen bonds: A:F.144, A:S.148, A:H.168, A:E.170, A:E.170, A:Q.193, A:Q.193 Water bridges: A:G.147, A:G.147 UO9.3: 16 residues within 4Å: Chain B: H.45, M.53, 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: URR.4 8 PLIP interactions: 8 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, B:Q.193 Water bridges: B:G.147

2 x URR: N~2~-(ethoxycarbonyl)-N-{(1S,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide(Covalent)

URR.2: 18 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, P.172, H.176, D.191, Q.193, T.194, A.195 Ligands: UO9.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.45, 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:E.170, A:Q.193, A:Q.193 URR.4: 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: UO9.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:H.45, B:M.169 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

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 2 PLIP interactions: 2 interactions with chain B 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

2022-09-07

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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