SMTL ID : 8czv.1

Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 17d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x P8C: [(1~{S},2~{R})-2-[4,4-bis(fluoranyl)cyclohexyl]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)

P8C.1: 19 residues within 4Å: Chain A: H.48, L.56, F.150, L.151, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, H.182, D.197, K.198, Q.199, V.200, H.201 Ligands: PJR.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.48, A:L.56, A:M.175, A:A.178 Hydrogen bonds: A:Q.174, A:E.176, A:E.176, A:Q.199 Water bridges: A:G.153 P8C.3: 19 residues within 4Å: Chain B: H.48, L.56, F.150, L.151, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, H.182, D.197, K.198, Q.199, V.200, H.201 Ligands: PJR.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.48, B:L.56, B:M.175, B:A.178 Hydrogen bonds: B:Q.174, B:E.176, B:E.176, B:Q.199 Water bridges: B:G.153

2 x PJR: [(1~{S},2~{R})-2-[4,4-bis(fluoranyl)cyclohexyl]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)

PJR.2: 21 residues within 4Å: Chain A: H.48, L.56, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, H.182, D.197, K.198, Q.199, V.200, H.201 Ligands: P8C.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.48, A:M.175 Hydrogen bonds: A:F.150, A:G.153, A:S.154, A:S.154, A:C.155, A:Q.174, A:E.176, A:Q.199 PJR.4: 21 residues within 4Å: Chain B: H.48, L.56, F.150, L.151, C.152, G.153, S.154, C.155, H.173, Q.174, M.175, E.176, L.177, A.178, H.182, D.197, K.198, Q.199, V.200, H.201 Ligands: P8C.3 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.48, B:M.175 Hydrogen bonds: B:F.150, B:G.153, B:S.154, B:S.154, B:C.155, B:Q.174, B:E.176, 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

2022-06-22

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3C-like proteinase

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