2XYA: Non-covalent inhibtors of rhinovirus 3C protease

Non-covalent inhibtors of rhinovirus 3C protease. Determined by X-ray diffraction at 2.4 Å resolution. Released 27 Apr 2011.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: HUMAN RHINOVIRUS SP.
Chains: 1
Atoms: 1,462
Mol. weight: 20.35 kDa
Ligands: 7L4
Released: 27 Apr 2011

Explore 2XYA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XYA contains 7 α-helices and 15 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, 15 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	52-55	4	1
β-strand	59-63	5	1
β-strand	69-76	8	1
β-strand	83	1	2
α-helix	87-89	3
β-strand	97-104	8	3
β-strand	112-123	12	3
α-helix	124-125	2
β-strand	134-139	6	3
α-helix	144-146	3
α-helix	149	1
β-strand	150-153	4	3
β-strand	156-164	9	3
β-strand	168-173	6	3
α-helix	176-178	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Picornain 3C	A	protein	182	HUMAN RHINOVIRUS SP.	P04936 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2XYA_1 PICORNAIN 3C (chains A)
GSGPEEEFGMSLIKHNSCVITTENGKFTGLGVYDRFVVVPTHADPGKEIQVDGITTKVID
SYDLYNKNGIKLEITVLKLDRNEKFRDIRRYIPNNEDDYPNCNLALLANQPEPTIINVGD
VVSYGNILLSGNQTARMLKYSYPTKSGYCGGVLYKIGQVLGIHVGGNGRDGFSAMLLRSY
FT

Ligands and cofactors

ID	Name	Formula	Copies
7L4	2-phenylquinolin-4-ol	C15 H11 N O	1

Primary citation

Non-Covalent Inhibitors of Rhinovirus 3C Protease. Baxter, A., Chambers, M., Edfeldt, F. et al. Bioorg Med Chem Lett (2011) 21:777. DOI 10.1016/J.BMCL.2010.11.110 · 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
6FFS 1.86 Å, Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease…
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
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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