1UUD

NMR structure of a synthetic small molecule, rbt203, bound to HIV-1 TAR RNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRRAINT VIOLATION ENERGY 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rational Design of Inhibitors of HIV-1 Tar RNA Through the Stabilisation of Electrostatic "Hot Spots"

Davis, B.Afshar, M.Varani, G.Murchie, A.I.H.Karn, J.Lentzen, G.Drysdale, M.J.Bower, J.Potter, A.J.Aboul-Ela, F.

(2004) J Mol Biol 336: 343

  • DOI: 10.1016/j.jmb.2003.12.046
  • Primary Citation of Related Structures:  
    1UUD, 1UUI

  • PubMed Abstract: 
  • The targeting of RNA for the design of novel anti-viral compounds has until now proceeded largely without incorporating direct input from structure-based design methodology, partly because of lack of structural data, and complications arising from substrate flexibility ...

    The targeting of RNA for the design of novel anti-viral compounds has until now proceeded largely without incorporating direct input from structure-based design methodology, partly because of lack of structural data, and complications arising from substrate flexibility. We propose a paradigm to explain the physical mechanism for ligand-induced refolding of trans-activation response element (TAR RNA) from human immunodeficiency virus 1 (HIV-1). Based upon Poisson-Boltzmann analysis of the TAR structure, as bound by a peptide derived from the transcriptional activator protein, Tat, our hypothesis shows that two specific electrostatic interactions are necessary to stabilise the conformation. This result contradicts the belief that a single argininamide residue is responsible for stabilising the TAR fold, as well as the conventional wisdom that electrostatic interactions with RNA are non-specific or dominated by phosphates. We test this hypothesis by using NMR and computational methods to model the interaction of a series of novel inhibitors of the in vitro RNA-binding activities for a peptide derived from Tat. A subset of inhibitors, including the bis-guanidine compound rbt203 and its analogues, induce a conformation in TAR similar to that brought about by the protein. Comparison of the interactions of two of these ligands with the RNA and structure-activity relationships observed within the compound series, confirm the importance of the two specific electrostatic interactions in the stabilisation of the Tat-bound RNA conformation. This work illustrates how the use of medicinal chemistry and structural analysis can provide a rational basis for prediction of ligand-induced conformational change, a necessary step towards the application of structure-based methods in the design of novel RNA or protein-binding drugs.


    Related Citations: 
    • The Structure of the Human Immunodeficiency Virus Recognition by Tat Protein
      Aboul-Ela, F., Jkarn, J., Varani, G.
      (1995) J Mol Biol 253: 313

    Organizational Affiliation

    RiboTargets Ltd, Granta Park, Abington, CB1 6GB, Cambridge, UK.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3')A [auth B]29HIV-1 M:B_HXB2R
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P14
Query on P14

Download Ideal Coordinates CCD File 
B N-[2-(2-{[(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)AMINO]METHYL}-4-METHOXYPHENOXY)ETHYL]GUANIDINE
C16 H31 N7 O2
ZCQAXURCNFAREC-UHFFFAOYSA-P
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
P14 PDBBind:  1UUD Ki: 1540 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRRAINT VIOLATION ENERGY 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance