Inhibitor Induced Structural Change in the HCV IRES Domain IIa RNA

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 16 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

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Inhibitor-induced structural change in the HCV IRES domain IIa RNA.

Paulsen, R.B.Seth, P.P.Swayze, E.E.Griffey, R.H.Skalicky, J.J.Cheatham, T.E.Davis, D.R.

(2010) Proc Natl Acad Sci U S A 107: 7263-7268

  • DOI: https://doi.org/10.1073/pnas.0911896107
  • Primary Citation of Related Structures:  
    2KTZ, 2KU0

  • PubMed Abstract: 

    Translation of the hepatitis C virus (HCV) RNA is initiated from a highly structured internal ribosomal entry site (IRES) in the 5' untranslated region (5' UTR) of the RNA genome. An important structural feature of the native RNA is an approximately 90 degrees helical bend localized to domain IIa that positions the apical loop of domain IIb of the IRES near the 40S ribosomal E-site to promote eIF2-GDP release, facilitating 80S ribosome assembly. We report here the NMR structure of a domain IIa construct in complex with a potent small-molecule inhibitor of HCV replication. Molecular dynamics refinement in explicit solvent and subsequent energetic analysis indicated that each inhibitor stereoisomer bound with comparable affinity and in an equivalent binding mode. The in silico analysis was substantiated by fluorescence-based assays showing that the relative binding free energies differed by only 0.7 kcal/mol. Binding of the inhibitor displaces key nucleotide residues within the bulge region, effecting a major conformational change that eliminates the bent RNA helical trajectory, providing a mechanism for the antiviral activity of this inhibitor class.

  • Organizational Affiliation

    Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.

Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
HCV IRES Domain IIa RNA38Hepacivirus hominis
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ISH

Download Ideal Coordinates CCD File 
B [auth A](7R)-7-[(dimethylamino)methyl]-1-[3-(dimethylamino)propyl]-7,8-dihydro-1H-furo[3,2-e]benzimidazol-2-amine
C17 H27 N5 O
Binding Affinity Annotations 
IDSourceBinding Affinity
ISH PDBBind:  2KTZ Kd: 9000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 16 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-05-22
    Changes: Data collection