8D28

Crystal structure of theophylline aptamer in complex with theophylline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of small molecules that target a tertiary-structured RNA.

Menichelli, E.Lam, B.J.Wang, Y.Wang, V.S.Shaffer, J.Tjhung, K.F.Bursulaya, B.Nguyen, T.N.Vo, T.Alper, P.B.McAllister, C.S.Jones, D.H.Spraggon, G.Michellys, P.Y.Joslin, J.Joyce, G.F.Rogers, J.

(2022) Proc Natl Acad Sci U S A 119: e2213117119-e2213117119

  • DOI: https://doi.org/10.1073/pnas.2213117119
  • Primary Citation of Related Structures:  
    8D28, 8D29, 8D2A, 8D2B, 8D5L, 8D5O, 8DK7

  • PubMed Abstract: 

    There is growing interest in therapeutic intervention that targets disease-relevant RNAs using small molecules. While there have been some successes in RNA-targeted small-molecule discovery, a deeper understanding of structure-activity relationships in pursuing these targets has remained elusive. One of the best-studied tertiary-structured RNAs is the theophylline aptamer, which binds theophylline with high affinity and selectivity. Although not a drug target, this aptamer has had many applications, especially pertaining to genetic control circuits. Heretofore, no compound has been shown to bind the theophylline aptamer with greater affinity than theophylline itself. However, by carrying out a high-throughput screen of low-molecular-weight compounds, several unique hits were identified that are chemically distinct from theophylline and bind with up to 340-fold greater affinity. Multiple atomic-resolution X-ray crystal structures were determined to investigate the binding mode of theophylline and four of the best hits. These structures reveal both the rigidity of the theophylline aptamer binding pocket and the opportunity for other ligands to bind more tightly in this pocket by forming additional hydrogen-bonding interactions. These results give encouragement that the same approaches to drug discovery that have been applied so successfully to proteins can also be applied to RNAs.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, San Diego, CA 92121.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (33-MER)A [auth B],
B [auth A]
33synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TEP (Subject of Investigation/LOI)
Query on TEP

Download Ideal Coordinates CCD File 
C [auth B],
J [auth A]
THEOPHYLLINE
C7 H8 N4 O2
ZFXYFBGIUFBOJW-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth B],
E [auth B],
F [auth B],
G [auth B],
L [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
K [auth A],
M [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.074α = 95.73
b = 29.561β = 90.09
c = 80.397γ = 109.58
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description