6FFS: 3C Protease

Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors. Determined by X-ray diffraction at 1.86 Å resolution. Released 21 Feb 2018.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Human rhinovirus 2
Chains: 1
Atoms: 1,718
Mol. weight: 20.75 kDa
Ligands: D8E
Released: 21 Feb 2018

Explore 6FFS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FFS contains 7 α-helices and 14 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
β-strand	15-20	6	1
β-strand	23-31	9	1
β-strand	32	1	2
β-strand	34-38	5	1
α-helix	39-41	3
β-strand	46-49	4	1
β-strand	52-63	12	1
β-strand	69-77	9	1
β-strand	83	1	2
α-helix	87-89	3
β-strand	97-104	8	3
β-strand	112-127	16	3
β-strand	130-138	9	3
α-helix	144-146	3
α-helix	149	1
β-strand	150-153	4	3
β-strand	156-164	9	3
β-strand	169-173	5	3
α-helix	174	1
α-helix	176-178	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3C Protease	A	protein	182	Human rhinovirus 2	P04936 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6FFS_1 3C Protease (chains A)
GSGPEEEFGMSLIKHNSCVITTENGKFTGLGVYDRFVVVPTHADPGKEIQVDGITTKVID
SYDLYNKNGIKLEITVLKLDRNEKFRDIRRYIPNNEDDYPNCNLALLANQPEPTIINVGD
VVSYGNILLSGNQTARMLKYSYPTKSGYCGGVLYKIGQVLGIHVGGNGRDGFSAMLLRSY
FT

Ligands and cofactors

ID	Name	Formula	Copies
D8E	~{N}-[(2~{S},5~{S},14~{S})-2-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-9-methy…	C26 H34 F N5 O6	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors. Namoto, K., Sirockin, F., Sellner, H. et al. Bioorg Med Chem Lett (2018) 28:906-909. DOI 10.1016/j.bmcl.2018.01.064 · PubMed

Other PDB entries of the same protein (UniProt P04936 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5FX6 1.45 Å, Novel inhibitors of human rhinovirus 3C protease
5FX5 1.7 Å, Novel inhibitors of human rhinovirus 3C protease
6FFN 1.75 Å, Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease…
9W3O 1.76 Å, Crystal Structure of Human rhinovirus A2 3C Protease in Complex with a Broad-spectrum…
1CQQ 1.85 Å, Type 2 rhinovirus 3C protease with AG7088 inhibitor
2HRV 1.95 Å, 2A cysteine proteinase from human rhinovirus 2
1A3R 2.1 Å, FAB fragment (antibody 8F5) complexed with peptide from human rhinovirus (serotype 2)…
7ARA 2.24 Å, Rhinovirus A2 2A protease in complex with zVAM.fmk
2XYA 2.4 Å, Non-covalent inhibtors of rhinovirus 3C protease.
1FPN 2.6 Å, Human rhinovirus serotype 2 (HRV2)
3TN9 3.0 Å, X-ray structure of the HRV2 empty capsid (B-particle)
3VDD 3.2 Å, Structure of HRV2 capsid complexed with antiviral compound BTA798

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