SMTL ID : 8czw.1

Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 15d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x P8U: [(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{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)

P8U.1: 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, H.176, D.191, R.192, Q.193, T.194, A.195 Ligands: P8L.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.45, A:D.191, A:Q.193 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 Water bridges: A:Q.193, A:Q.193 P8U.3: 16 residues within 4Å: Chain B: H.45, M.53, 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: P8L.4 10 PLIP interactions: 10 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

2 x P8L: [(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},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)

P8L.2: 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, H.176, D.191, R.192, Q.193, T.194, A.195 Ligands: P8U.1 7 PLIP interactions: 7 interactions with chain A 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 P8L.4: 15 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, Q.193 Ligands: P8U.3 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 Water bridges: B:G.147, B:G.147

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., Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies. Acs Pharmacol Transl Sci (2023)

Release Date

2022-06-22

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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