1VRH

HRV14/SDZ 880-061 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthesis and activity of piperazine-containing antirhinoviral agents and crystal structure of SDZ 880-061 bound to human rhinovirus 14.

Oren, D.A.Zhang, A.Nesvadba, H.Rosenwirth, B.Arnold, E.

(1996) J Mol Biol 259: 120-134

  • DOI: 10.1006/jmbi.1996.0307
  • Primary Citation of Related Structures:  
    1VRH

  • PubMed Abstract: 
  • A series of antipicornaviral agents containing piperazinyl moieties was synthesized with the objective of obtaining a compound with a broad spectrum of antirhinovirus activity, high potency (< or = 0.003 microgram/ml), and low cytotoxicity (> or = 30 micrograms/ml) ...

    A series of antipicornaviral agents containing piperazinyl moieties was synthesized with the objective of obtaining a compound with a broad spectrum of antirhinovirus activity, high potency (< or = 0.003 microgram/ml), and low cytotoxicity (> or = 30 micrograms/ml). Five compounds of this series were evaluated in detail for efficacy against various HRV serotypes. The agent SDZ 880-061, containing the benzothiazine moiety SDZ 108-075, which is particularly active against HRV14, and the thiazolyl acetic acid ester group of SDZ 89-124, which is potent against HRV1B, indeed has a relatively broad antiviral spectrum. SDZ 880-061 inhibited 85% of 89 HRV serotypes tested at a concentration of < or = 3 micrograms/ml. The 3.0 A resolution X-ray structure of SDZ 880-061 bound to HRV14 has revealed the binding characteristics of this potent compound. It binds in the same pocket as other capsid-binding antiviral agents characterized to date, leaving the innermost portion of the pocket vacant. The binding causes similar, although less extensive, alterations of the HRV14 VP1 backbone conformation (residues 100 to 110, 151 to 159, and 213 to 224) compared to other antiviral agents analyzed structurally. Although the contacts between SDZ 880-061 and HRV14 are mostly of hydrophobic character, the inhibitor has three relatively short polar interactions with residues of VP1 that represent potential hydrogen bonds. The amount of solvent-accessible surface area of SDZ 880-061 buried in the complex (613 A2) is within the range of that observed in protein-protein interfaces. The observed influence of time of addition or removal of SDZ 880-061 on virus yield and on the infectious-center formation indicates that the compound primarily interferes with HRV14 cellular attachment. Since it is assumed that uncoating requires virion instability and/or flexibility, the finding that SDZ 880-061 has only a marginal effect on uncoating may be due to the fact that it does not completely fill the hydrophobic pocket.


    Related Citations: 
    • Sdz 35-682, a New Picornavirus Capsid-Binding Agent with Potent Antiviral Activity
      Rosenwirth, B., Oren, D.A., Arnold, E., Kis, Z.L., Eggers, H.J.
      (1995) Antiviral Res 26: 65
    • 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., al., et
      (1993) J Mol Biol 230: 857
    • 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 A
      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., al., et
      (1985) Nature 317: 145

    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM), Piscastaway, NJ, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RHINOVIRUS 14 1289Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RHINOVIRUS 14 2262Rhinovirus B14Mutation(s): 1 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03303 (Human rhinovirus 14)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RHINOVIRUS 14 3236Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RHINOVIRUS 14 468Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SD8
Query on SD8

Download Ideal Coordinates CCD File 
1
2-[4-(2H-1,4-BENZOTHIAZINE-3-YL)-PIPERAZINE-1-LY]-1,3-THIAZOLE-4-CARBOXYLIC ACID ETHYLESTER
C18 H20 N4 O2 S2
AQJQFCRTSWIUCY-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
PURDUEdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance