SMTL ID : 6ffn.1

Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x D8K: ~{N}-[(5~{S},8~{S},11~{S},15~{R})-8-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-2,7,10,14-tetrakis(oxidanylidene)-1,6,9,13-tetrazabicyclo[13.3.0]octadecan-11-yl]-5-methyl-1,2-oxazole-3-carboxamide(Covalent)

D8K.1: 18 residues within 4Å: Chain A: F.27, H.42, E.73, L.128, L.129, S.130, N.132, T.144, K.145, S.146, C.149, H.163, V.164, G.165, G.166, N.167, G.168, F.172 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.42, A:E.73, A:L.129, A:L.129, A:L.129, A:F.172 Hydrogen bonds: A:S.130, A:S.130, A:V.164, A:G.166, A:G.166, A:G.166 Water bridges: A:G.131, A:C.149

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: N.66, K.67, E.96, R.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.66, A:K.67 Salt bridges: A:K.67, A:R.136

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 6 residues within 4Å: Chain A: T.21, T.22, E.23, E.48, I.49, Q.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.50 Salt bridges: A:E.23

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: S.11, L.12, H.15, N.16, R.86, I.88, Y.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.11, A:N.16, A:R.86 Water bridges: A:R.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Namoto, K. et al., Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors. Bioorg. Med. Chem. Lett. (2018)

Release Date

2018-02-21

Peptides

3C protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3C protease

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