6BFB

Crystal structure of a F. nucleatum FMN riboswitch bound to WG-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry.

Rizvi, N.F.Howe, J.A.Nahvi, A.Klein, D.J.Fischmann, T.O.Kim, H.Y.McCoy, M.A.Walker, S.S.Hruza, A.Richards, M.P.Chamberlin, C.Saradjian, P.Butko, M.T.Mercado, G.Burchard, J.Strickland, C.Dandliker, P.J.Smith, G.F.Nickbarg, E.B.

(2018) ACS Chem Biol 13: 820-831

  • DOI: 10.1021/acschembio.7b01013
  • Primary Citation of Related Structures:  
    6BFB

  • PubMed Abstract: 
  • Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA ...

    Recent advances in understanding the relevance of noncoding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA. Here, we report the first application of the Automated Ligand Detection System (ALIS), an indirect AS-MS technique, for the selective detection of small molecule-ncRNA interactions, high-throughput screening against large unbiased small-molecule libraries, and identification and characterization of novel compounds (structurally distinct from both FMN and ribocil) that target the FMN riboswitch. Crystal structures reveal that different compounds induce various conformations of the FMN riboswitch, leading to different activity profiles. Our findings validate the ALIS platform for HTS screening for RNA-binding small molecules and further demonstrate that ncRNA can be broadly targeted by chemically diverse yet selective small molecules as therapeutics.


    Organizational Affiliation

    Merck & Co., Inc. , Boston , Massachusetts 02115 , United States.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (54-MER)A [auth X]54Fusobacterium nucleatum
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (56-MER)B [auth Y]56Fusobacterium nucleatum
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DKM (Subject of Investigation/LOI)
Query on DKM

Download Ideal Coordinates CCD File 
C [auth X]5-[(3S,4S)-3-(dimethylamino)-4-hydroxypyrrolidin-1-yl]-6-fluoro-4-methyl-8-oxo-3,4-dihydro-8H-1-thia-4,9b-diazacyclopenta[cd]phenalene-9-carboxylic acid
C20 H21 F N4 O4 S
JHSMWPKZVMQLKB-STQMWFEESA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth X]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.13α = 90
b = 71.13β = 90
c = 141.19γ = 120
Software Package:
Software NamePurpose
autoBUSTERrefinement
XDSdata reduction
AutoPROCdata scaling
autoBUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references