1VRH

HRV14/SDZ 880-061 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 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

  • 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 ...

    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: 
    • 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
    • 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.,Sect.A 44: 270
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHINOVIRUS 14
1
289Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RHINOVIRUS 14
2
262Human rhinovirus 14Mutation(s): 1 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RHINOVIRUS 14
3
236Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RHINOVIRUS 14
4
68Human rhinovirus 14Mutation(s): 0 
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SD8
Query on SD8

Download SDF File 
Download CCD File 
1
2-[4-(2H-1,4-BENZOTHIAZINE-3-YL)-PIPERAZINE-1-LY]-1,3-THIAZOLE-4-CARBOXYLIC ACID ETHYLESTER
SDZ 880-061
C18 H20 N4 O2 S2
AQJQFCRTSWIUCY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 445.100α = 90.00
b = 445.100β = 90.00
c = 445.100γ = 90.00
Software Package:
Software NamePurpose
PURDUEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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