1CQQ: Type 2 rhinovirus 3C protease

Type 2 rhinovirus 3C protease with AG7088 inhibitor. Determined by X-ray diffraction at 1.85 Å resolution. Released 20 Sept 1999.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Human rhinovirus 2
Chains: 1
Atoms: 1,654
Mol. weight: 20.58 kDa
Ligands: AG7
Released: 20 Sept 1999

Explore 1CQQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1CQQ contains 5 α-helices and 16 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: 5 helices, 16 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	86-89	4
β-strand	97-104	8	3
β-strand	112-121	10	3
β-strand	125-127	3	1
β-strand	130-132	3	1
β-strand	135-138	4	3
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
Type 2 rhinovirus 3C protease	A	protein	180	Human rhinovirus 2	P04936 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1CQQ_1 TYPE 2 RHINOVIRUS 3C PROTEASE (chains A)
GPEEEFGMSLIKHNSCVITTENGKFTGLGVYDRFVVVPTHADPGKEIQVDGITTKVIDSY
DLYNKNGIKLEITVLKLDRNEKFRDIRRYIPNNEDDYPNCNLALLANQPEPTIINVGDVV
SYGNILLSGNQTARMLKYSYPTKSGYCGGVLYKIGQVLGIHVGGNGRDGFSAMLLRSYFT

Ligands and cofactors

ID	Name	Formula	Copies
AG7	4-{2-(4-fluoro-benzyl)-6-methyl-5-[(5-methyl-isoxazole-3-carbonyl)-amino]-4-oxo…	C31 H41 F N4 O7	1

Primary citation

Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Matthews, D.A., Dragovich, P.S., Webber, S.E. et al. Proc Natl Acad Sci U S A (1999) 96:11000-11007. DOI 10.1073/pnas.96.20.11000 · 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…
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
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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