SMTL ID : 8dgy.1

Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 16d (high resolution)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x S9U: [(1~{R},2~{R})-2-(cyclohexylmethyl)cyclopropyl]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)

S9U.1: 20 residues within 4Å: Chain A: H.48, L.56, Y.61, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, A.178, H.182, D.197, K.198, Q.199, H.201 Ligands: SD6.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.56, A:M.175, A:A.178, A:Q.199, A:H.201 Hydrogen bonds: A:G.153, A:S.154, A:C.155, A:Q.174, A:E.176, A:E.176, A:E.176, A:Q.199 Water bridges: A:Q.199 S9U.3: 20 residues within 4Å: Chain B: H.48, L.56, Y.61, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, A.178, H.182, D.197, K.198, Q.199, H.201 Ligands: SD6.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.56, B:M.175, B:A.178, B:Q.199, B:H.201 Hydrogen bonds: B:G.153, B:S.154, B:C.155, B:Q.174, B:E.176, B:E.176, B:Q.199 Water bridges: B:Q.199

2 x SD6: [(1~{R},2~{R})-2-(cyclohexylmethyl)cyclopropyl]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)

SD6.2: 19 residues within 4Å: Chain A: H.48, L.56, Y.61, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, A.178, H.182, D.197, K.198, Q.199, H.201 Ligands: S9U.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.56, A:M.175, A:A.178, A:Q.199, A:H.201 Hydrogen bonds: A:Q.174, A:E.176, A:E.176, A:E.176, A:Q.199 Water bridges: A:G.153, A:Q.199 SD6.4: 19 residues within 4Å: Chain B: H.48, L.56, Y.61, F.150, L.151, C.152, S.154, C.155, H.173, Q.174, M.175, E.176, A.178, H.182, D.197, K.198, Q.199, H.201 Ligands: S9U.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.56, B:M.175, B:A.178, B:Q.199, B:H.201 Hydrogen bonds: B:Q.174, B:E.176, B:E.176, B:Q.199 Water bridges: B:G.153, B:Q.199

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

2022-07-06

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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