1VBD

POLIOVIRUS (TYPE 1, MAHONEY STRAIN) COMPLEXED WITH R78206


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.287 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structures of poliovirus complexes with anti-viral drugs: implications for viral stability and drug design.

Grant, R.A.Hiremath, C.N.Filman, D.J.Syed, R.Andries, K.Hogle, J.M.

(1994) Curr Biol 4: 784-797

  • DOI: https://doi.org/10.1016/s0960-9822(00)00176-7

  • PubMed Abstract: 

    Picornaviruses, such as the structurally related polioviruses and rhinoviruses, are important human pathogens which have been the target of major drug development efforts. Receptor-mediated uncoating and thermal inactivation of poliovirus and rhinovirus are inhibited by agents that bind to each virus by inserting into a pocket in the beta barrel of the viral capsid protein, VP1. This pocket, which is normally empty in human rhinovirus-14 (HRV14), is occupied by an unknown natural ligand in poliovirus. Structural studies of HRV14-drug complexes have shown that drug binding causes large, localized changes in the conformation of VP1. We report the crystal structures of six complexes between poliovirus and capsid-binding, antiviral drugs, including complexes of four different drugs with the Sabin vaccine strain of type 3 poliovirus, and complexes of one of these drugs with two other poliovirus strains that contain sequence differences in the drug-binding site. In each complex, the changes in capsid structure associated with drug binding are limited to minor adjustments in the conformations of a few side chains lining the binding site. The minor structural changes caused by drug binding suggest a model of drug action in which it is the conformational changes prevented by the bound drug, rather than obvious conformational changes induced by drug binding, which exert the biological effect. Our results, along with additional structures of rhinovirus-drug complexes, suggest possible improvements in drug design, and provide important clues about the nature of the conformational changes that are involved in the uncoating process.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLIOVIRUS TYPE 1 MAHONEYA [auth 0]5Human poliovirus 1 MahoneyMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
POLIOVIRUS TYPE 1 MAHONEYB [auth 1]302Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
POLIOVIRUS TYPE 1 MAHONEYC [auth 2]272Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
POLIOVIRUS TYPE 1 MAHONEYD [auth 3]238Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
POLIOVIRUS TYPE 1 MAHONEYE [auth 4]68Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J78
Query on J78

Download Ideal Coordinates CCD File 
F [auth 1](METHYLPYRIDAZINE PIPERIDINE PROPYLOXYPHENYL)ETHYLACETATE
C22 H29 N3 O3
UEIUDEUUVLYRFV-UHFFFAOYSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
G [auth 4]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.287 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 322.94α = 90
b = 358.04β = 90
c = 380.15γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2023-04-19
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2024-11-20
    Changes: Data collection, Structure summary