1HRI

STRUCTURE DETERMINATION OF ANTIVIRAL COMPOUND SCH 38057 COMPLEXED WITH HUMAN RHINOVIRUS 14

DOI: 10.2210/pdb1HRI/pdb

Classification: VIRUS
Organism(s): Rhinovirus B14
Expression System: Homo sapiens
Mutation(s): No

Deposited: 1992-10-01 Released: 1993-10-31
Deposition Author(s): Zhang, A., Nanni, R.G., Oren, D.A., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure determination of antiviral compound SCH 38057 complexed with human rhinovirus 14.

Zhang, A., Nanni, R.G., Li, T., Arnold, G.F., Oren, D.A., Jacobo-Molina, A., Williams, R.L., Kamer, G., Rubenstein, D.A., Li, Y., Rozhon, E., Cox, S., Buontempo, P., O'Connell, J., Schwartz, J., Miller, G., Bauer, B., Versace, R., Pinto, P., Ganguly, A., Girijavallabhan, V., Arnold, E.

(1993) J Mol Biol 230: 857-867

PubMed: 8386772 Search on PubMed
DOI: 10.1006/jmbi.1993.1206
Primary Citation of Related Structures:
1HRI

PubMed Abstract:

SCH 38057 (1-[6-(2-chloro-4-methoxyphenoxy)-hexyl]imidazole hydrochloride) is a new, water-soluble antiviral compound that has inhibitory activities against a number of picornavirus infections. The structure of the human rhinovirus 14 (HRV14) complex with SCH 38057 was determined at 3.0 A resolution by single-crystal diffraction techniques using synchrotron X-radiation. SCH 38057 was found to bind at the innermost end of the hydrophobic pocket within the capsid protein VP1, a locus of binding of other antipicornaviral agents; however, the complex differs from previously reported complexes in two important aspects. It leaves a considerable volume near the entrance to the binding pocket unoccupied. In addition, the alterations in the conformation of the VP1 polypeptide are similar to, but more extensive than those observed in HRV14 complexes with other antiviral agents. Although only 9 amino acids of VP1 have close contacts with the SCH 38057 molecule (within 3.6 A), at least 36 amino acids from both VP1 and VP3 have significantly altered conformations (C alpha movement > 0.5 A versus native). The structures of complexes of HRV14 with SCH 38057 and WIN 51711 are compared. Aromatic ring interactions between picornavirus capsid residues and antiviral inhibitors are proposed to be among the major determinants for positioning of these compounds.

Related Citations:

Sch 38057: A Picornavirus Capsid-Binding Molecule with Antiviral Activity After the Initial Stage of Viral Uncoating
Rozhon, E., Cox, S., Buontempo, P., O'Connell, J., Slater, W., De Martino, J., Schwartz, J., Miller, G., Arnold, E., Zhang, A., Morrow, C., Jablonski, S., Pinto, P., Versace, R., Duelfer, T., Girijavallabhan, V.
() To be published --: --

Three-Dimensional Structure-Activity Relationships for Antiviral Agents that Interact with Picornavirus Capsids
Zhang, A., Nanni, R.G., Oren, D.A., Rozhon, E.J., Arnold, E.
(1992) Semin Virol 3: 453

Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 Angstroms
Arnold, E., Rossmann, M.G.
(1990) J Mol Biol 211: 763

The Use of Molecular-Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure
Arnold, E., Rossmann, M.G.
(1988) Acta Crystallogr A 44: 270

Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Rossmann, M.G., Arnold, E., Erickson, J.W., Frankenberger, E.A., Griffith, J.P., Hecht, H.-J., Johnson, J.E., Kamer, G., Luo, M., Mosser, A.G., Rueckert, R.R., Sherry, B., Vriend, G.
(1985) Nature 317: 145

Organizational Affiliation:

Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ 08854-5638.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)	A [auth 1]	289	Rhinovirus B14	Mutation(s): 0 EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03303 (Human rhinovirus 14) Explore P03303 Go to UniProtKB: P03303
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)	B [auth 2]	262	Rhinovirus B14	Mutation(s): 0 EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03303 (Human rhinovirus 14) Explore P03303 Go to UniProtKB: P03303
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)	C [auth 3]	236	Rhinovirus B14	Mutation(s): 0 EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03303 (Human rhinovirus 14) Explore P03303 Go to UniProtKB: P03303
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)	D [auth 4]	68	Rhinovirus B14	Mutation(s): 0 EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03303 (Human rhinovirus 14) Explore P03303 Go to UniProtKB: P03303
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S57 Query on S57 Download Ideal Coordinates CCD File SDF format, chain E [auth 1] MOL2 format, chain E [auth 1]	E [auth 1]	1-[6-(2-CHLORO-4-METHYXYPHENOXY)-HEXYL]-IMIDAZOLE C₁₆ H₂₁ Cl N₂ O₂ UKVVEWLDHJDSNJ-UHFFFAOYSA-N		Ligand Interaction