1UTS

Designed HIV-1 TAR Binding Ligand


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 16 
  • Selection Criteria: LEAST RESTRAINT VIOLATION ENERGY 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA.

Murchie, A.I.Davis, B.Isel, C.Afshar, M.Drysdale, M.J.Bower, J.Potter, A.J.Starkey, I.D.Swarbrick, T.M.Mirza, S.Prescott, C.D.Vaglio, P.Aboul-ela, F.Karn, J.

(2004) J Mol Biol 336: 625-638

  • DOI: 10.1016/j.jmb.2003.12.028
  • Primary Citation of Related Structures:  
    1UTS

  • PubMed Abstract: 
  • The targeting of RNA for the design of novel anti-viral compounds represents an area of vast potential. We have used NMR and computational methods to model the interaction of a series of synthetic inhibitors of the in vitro RNA binding activities of a peptide derived from the transcriptional activator protein, Tat, from human immunodeficiency virus type 1 ...

    The targeting of RNA for the design of novel anti-viral compounds represents an area of vast potential. We have used NMR and computational methods to model the interaction of a series of synthetic inhibitors of the in vitro RNA binding activities of a peptide derived from the transcriptional activator protein, Tat, from human immunodeficiency virus type 1. Inhibition has been measured through the monitering of fluorescence resonance energy transfer between fluorescently labeled peptide and RNA components. A series of compounds containing a bi-aryl heterocycle as one of the three substituents on a benzylic scaffold, induce a novel, inactive TAR conformation by stacking between base-pairs at the site of a three-base bulge within TAR. The development of this series resulted in an enhancement in potency (with Ki < 100 nM in an in vitro assay) and the removal of problematic guanidinium moieties. Ligands from this series can act as inhibitors of Tat-induced transcription in a cell-free system. This study validates the drug design strategy of using a ligand to target the RNA receptor in a non-functional conformation.


    Organizational Affiliation

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



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  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]29Human immunodeficiency virus 1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P13 (Subject of Investigation/LOI)
Query on P13

Download Ideal Coordinates CCD File 
BN-[2-(3-AMINOPROPOXY)-5-(1H-INDOL-5-YL)BENZYL]-N-(2-PIPERAZIN-1-YLETHYL)AMINE
C24 H33 N5 O
WVRJFVULANTNJW-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
P13 PDBBind:  1UTS Ki: 39 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 16 
  • Selection Criteria: LEAST RESTRAINT VIOLATION ENERGY 
  • OLDERADO: 1UTS Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-05-05
    Changes: Data collection, Database references, Other