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 2.2 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: https://doi.org/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). 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RHINOVIRUS 14A [auth 1]289rhinovirus B14Mutation(s): 0 
UniProt
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03303
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RHINOVIRUS 14B [auth 2]262rhinovirus B14Mutation(s): 1 
UniProt
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03303
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RHINOVIRUS 14C [auth 3]236rhinovirus B14Mutation(s): 0 
UniProt
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03303
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RHINOVIRUS 14D [auth 4]68rhinovirus B14Mutation(s): 0 
UniProt
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03303
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SD8
Query on SD8

Download Ideal Coordinates CCD File 
E [auth 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
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
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations, Other
  • Version 2.0: 2023-01-18
    Type: Remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2023-03-15
    Changes: Advisory
  • Version 2.2: 2024-05-22
    Changes: Data collection