3RIX

1.7A resolution structure of a firefly luciferase-Aspulvinone J inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Titration-based screening for evaluation of natural product extracts: identification of an aspulvinone family of luciferase inhibitors.

Cruz, P.G.Auld, D.S.Schultz, P.J.Lovell, S.Battaile, K.P.MacArthur, R.Shen, M.Tamayo-Castillo, G.Inglese, J.Sherman, D.H.

(2011) Chem.Biol. 18: 1442-1452

  • DOI: 10.1016/j.chembiol.2011.08.011

  • PubMed Abstract: 
  • The chemical diversity of nature has tremendous potential for the discovery of molecular probes and medicinal agents. However, sensitivity of HTS assays to interfering components of crude extracts derived from plants, and macro- and microorganisms ha ...

    The chemical diversity of nature has tremendous potential for the discovery of molecular probes and medicinal agents. However, sensitivity of HTS assays to interfering components of crude extracts derived from plants, and macro- and microorganisms has curtailed their use in lead discovery. Here, we describe a process for leveraging the concentration-response curves obtained from quantitative HTS to improve the initial selection of "actives" from a library of partially fractionated natural product extracts derived from marine actinomycetes and fungi. By using pharmacological activity, the first-pass CRC paradigm improves the probability that labor-intensive subsequent steps of reculturing, extraction, and bioassay-guided isolation of active component(s) target the most promising strains and growth conditions. We illustrate how this process identified a family of fungal metabolites as potent inhibitors of firefly luciferase, subsequently resolved in molecular detail by X-ray crystallography.


    Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Luciferin 4-monooxygenase
A
550Photinus pyralisMutation(s): 0 
EC: 1.13.12.7
Find proteins for P08659 (Photinus pyralis)
Go to UniProtKB:  P08659
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
923
Query on 923

Download SDF File 
Download CCD File 
A
(5Z)-4-hydroxy-3-[(2R)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-1-benzofuran-5-yl]-5-{[(2R)-2-(2-hydroxypropan-2-yl)-2,3-dihydro-1-benzofuran-5-yl]methylidene}furan-2(5H)-one
Aspulvinone J-CR
C27 H28 O7
YPXKKOMPEGAWMY-JQOCIHOLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.190 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 83.738α = 90.00
b = 83.738β = 90.00
c = 96.913γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
JDirectordata collection
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2012-12-05
    Type: Non-polymer description
  • Version 1.3: 2017-11-08
    Type: Refinement description