1HRV

HRV14/SDZ 35-682 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

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: 65-82

  • DOI: 10.1016/0166-3542(94)00066-h
  • Primary Citation of Related Structures:  
    1HRV

  • PubMed Abstract: 
  • SDZ 35-682 is a potent and selective inhibitor of the replication of members of the picornavirus group. It inhibits several rhinovirus serotypes and echovirus 9 at concentrations as low as 0.1 micrograms/ml, without exerting any effect on cell proliferation up to 30 micrograms/ml ...

    SDZ 35-682 is a potent and selective inhibitor of the replication of members of the picornavirus group. It inhibits several rhinovirus serotypes and echovirus 9 at concentrations as low as 0.1 micrograms/ml, without exerting any effect on cell proliferation up to 30 micrograms/ml. As observed with other capsid-binding antipicornavirus compounds, there is a wide variation in sensitivity of the different serotypes within the rhinovirus group. The point of interference of SDZ 35-682 in a single cycle of virus growth is an early event taking place before 2 or 3 h of echo- or rhinovirus replication, respectively. By incorporation of neutral red into the viral capsid and measurement of acquisition of photoresistance it is shown that uncoating of echovirus 9 is inhibited by SDZ 35-682. In addition, efficiency of adsorption of echovirus 9 is reduced by SDZ 35-682. To demonstrate that SDZ 35-682, like other uncoating inhibitors of picornaviruses, binds to the hydrophobic pocket beneath the canyon floor co-crystallization with HRV 14 was performed. Considerable conformational changes occur in VP1 in the HRV 14/SDZ 35-682 complex. SDZ 35-682 is 19 A long from end to end and thus fills the entire hydrophobic pocket including its innermost end; it is less flexible than other long antiviral agents. It has been suggested that compounds filling the entire hydrophobic pocket will affect the uncoating process of the virion. Thus, inhibition of viral uncoating, as demonstrated with echovirus 9, probably is the predominant mode of action of SDZ 35-682.


    Related Citations: 
    • 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
    • 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

    Sandoz Forschungsinstitut, Vienna, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
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
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Protein Feature View
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  • Reference Sequence
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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)
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Protein Feature View
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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)
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SDZ
Query on SDZ

Download Ideal Coordinates CCD File 
E [auth 1]1-[2-HYDROXY-3-(4-CYCLOHEXYL-PHENOXY)-PROPYL]-4-(2-PYRIDYL)-PIPERAZINE
C24 H33 N3 O2
BZJHCQBNFUNZPJ-QFIPXVFZSA-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
REFIrefinement
PURDUEdata reduction
Omodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-06-03
    Type: Initial release
  • Version 1.1: 2008-03-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance