5C45 | pdb_00005c45

Selective Small Molecule Inhibition of the FMN Riboswitch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 
    0.234 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Selective small-molecule inhibition of an RNA structural element.

Howe, J.A.Wang, H.Fischmann, T.O.Balibar, C.J.Xiao, L.Galgoci, A.M.Malinverni, J.C.Mayhood, T.Villafania, A.Nahvi, A.Murgolo, N.Barbieri, C.M.Mann, P.A.Carr, D.Xia, E.Zuck, P.Riley, D.Painter, R.E.Walker, S.S.Sherborne, B.de Jesus, R.Pan, W.Plotkin, M.A.Wu, J.Rindgen, D.Cummings, J.Garlisi, C.G.Zhang, R.Sheth, P.R.Gill, C.J.Tang, H.Roemer, T.

(2015) Nature 526: 672-677

  • DOI: https://doi.org/10.1038/nature15542
  • Primary Citation Related Structures: 
    5C45

  • PubMed Abstract: 

    Riboswitches are non-coding RNA structures located in messenger RNAs that bind endogenous ligands, such as a specific metabolite or ion, to regulate gene expression. As such, riboswitches serve as a novel, yet largely unexploited, class of emerging drug targets. Demonstrating this potential, however, has proven difficult and is restricted to structurally similar antimetabolites and semi-synthetic analogues of their cognate ligand, thus greatly restricting the chemical space and selectivity sought for such inhibitors. Here we report the discovery and characterization of ribocil, a highly selective chemical modulator of bacterial riboflavin riboswitches, which was identified in a phenotypic screen and acts as a structurally distinct synthetic mimic of the natural ligand, flavin mononucleotide, to repress riboswitch-mediated ribB gene expression and inhibit bacterial cell growth. Our findings indicate that non-coding RNA structural elements may be more broadly targeted by synthetic small molecules than previously expected.


  • Organizational Affiliation
    • Merck Research Laboratories, Kenilworth, New Jersey 07033, USA.

Macromolecule Content 

  • Total Structure Weight: 36.21 kDa 
  • Atom Count: 2,375 
  • Modeled Residue Count: 110 
  • Deposited Residue Count: 110 
  • Unique nucleic acid chains: 2

Macromolecules

Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
FMN RiboswitchA [auth X]54Fusobacterium nucleatum
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
FMN RiboswitchB [auth Y]56Fusobacterium nucleatum
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
51B

Query on 51B



Download:Ideal Coordinates CCD File
G [auth X](6M)-2-[(3S)-1-{[2-(methylamino)pyrimidin-5-yl]methyl}piperidin-3-yl]-6-(thiophen-2-yl)pyrimidin-4-ol
C19 H22 N6 O S
ZSXCVAIJFUEGJR-AWEZNQCLSA-N
K

Query on K



Download:Ideal Coordinates CCD File
C [auth X]
E [auth X]
F [auth X]
H [auth Y]
J [auth Y]
C [auth X],
E [auth X],
F [auth X],
H [auth Y],
J [auth Y],
K [auth Y]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth X],
I [auth Y]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free:  0.234 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.11α = 90
b = 71.11β = 90
c = 138.51γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2015-11-11
    Changes: Database references
  • Version 1.3: 2023-03-01
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description