6DN3

CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-activity relationship of flavin analogs that target the FMN riboswitch.

Vicens, Q.Mondragon, E.Reyes, F.E.Coish, P.Aristoff, P.Berman, J.Kaur, H.Kells, K.W.Wickens, P.Wilson, J.Gadwood, R.C.Schostarez, H.J.Suto, R.K.Blount, K.F.Batey, R.T.

(2018) ACS Chem. Biol. --: --

  • DOI: 10.1021/acschembio.8b00533
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The flavin mononucleotide (FMN) riboswitch is an emerging target for the development of novel RNA-targeting antibiotics. We previously discovered an FMN derivative -5FDQD- that protects mice against diarrhea-causing Clostridium difficile bacteria. He ...

    The flavin mononucleotide (FMN) riboswitch is an emerging target for the development of novel RNA-targeting antibiotics. We previously discovered an FMN derivative -5FDQD- that protects mice against diarrhea-causing Clostridium difficile bacteria. Here, we present the structure-based drug design strategy that led to the discovery of this fluoro-phenyl derivative with antibacterial properties. This approach involved the following stages: (1) structural analysis of all available free and bound FMN riboswitch structures; (2) design, synthesis and purification of derivatives; (3) in vitro testing for productive binding using two chemical probing methods; (4) in vitro transcription termination assays; (5) resolution of the crystal structures of the FMN riboswitch in complex with the most mature candidates. In the process, we delineated principles for productive binding to this riboswitch, thereby demonstrating the effectiveness of a coordinated structure-guided approach to designing drugs against RNA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA RIBOSWITCHX54Fusobacterium nucleatum
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (56-MER)Y56Fusobacterium nucleatum
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
Y
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
X, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GZ4
Query on GZ4

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Download CCD File 
Y
7,8-dimethyl-2,4-dioxo-10-(3-phenylpropyl)-1,2,3,4-tetrahydrobenzo[g]pteridin-10-ium
C21 H21 N4 O2
LVUMBLZQGDFTPC-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.550α = 90.00
b = 71.550β = 90.00
c = 140.270γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release