1LVJ

STRUCTURE OF TAR RNA COMPLEXED WITH A TAT-TAR INTERACTION NANOMOLAR INHIBITOR THAT WAS IDENTIFIED BY COMPUTATIONAL SCREENING


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 12 
  • Selection Criteria: least violations and lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening

Du, Z.Lind, K.E.James, T.L.

(2002) Chem Biol 9: 707-712

  • DOI: 10.1016/s1074-5521(02)00151-5
  • Primary Citation of Related Structures:  
    1LVJ

  • PubMed Abstract: 
  • HIV-1 TAR RNA functions critically in viral replication by binding the transactivating regulatory protein Tat. We recently identified several compounds that experimentally inhibit the Tat-TAR interaction completely at a 100 nM concentration. We used computational screening of the 181,000-compound Available Chemicals Directory against the three-dimensional structure of TAR [1] ...

    HIV-1 TAR RNA functions critically in viral replication by binding the transactivating regulatory protein Tat. We recently identified several compounds that experimentally inhibit the Tat-TAR interaction completely at a 100 nM concentration. We used computational screening of the 181,000-compound Available Chemicals Directory against the three-dimensional structure of TAR [1]. Here we report the NMR-derived structure of TAR complexed with acetylpromazine. This structure represents a new class of compounds with good bioavailability and low toxicity that bind with high affinity to TAR. NMR data unambiguously show that acetylpromazine binds only to the unique 5' bulge site to which the Tat protein binds. Specificity and affinity of binding are conferred primarily by a network of base stacking and hydrophobic interactions. Acetylpromazine alters the structure of free TAR less than Tat peptides and neomycin do.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Franciso, CA 94143, USA.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
HIV-1 Trans Activating Region RNAA31Human immunodeficiency virus 1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMZ
Query on PMZ

Download Ideal Coordinates CCD File 
B [auth A]1-[10-(3-DIMETHYLAMINO-PROPYL)-10H-PHENOTHIAZIN-2-YL]-ETHANONE
C19 H22 N2 O S
NOSIYYJFMPDDSA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 12 
  • Selection Criteria: least violations and lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations