1HRI

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

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

  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)A [auth 1]289rhinovirus B14Mutation(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)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03303
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)B [auth 2]262rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)C [auth 3]236rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)D [auth 4]68rhinovirus B14Mutation(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
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UniProt GroupP03303
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S57
Query on S57
Download Ideal Coordinates CCD File 
E [auth 1]1-[6-(2-CHLORO-4-METHYXYPHENOXY)-HEXYL]-IMIDAZOLE
C16 H21 Cl N2 O2
UKVVEWLDHJDSNJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 445.1α = 90
b = 445.1β = 90
c = 445.1γ = 90
Software Package:
Software NamePurpose
FRODOmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-02-22
    Changes: Database references