4E5D | pdb_00004e5d

2.2A resolution structure of a firefly luciferase-benzothiazole inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.232 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Firefly luciferase in chemical biology: a compendium of inhibitors, mechanistic evaluation of chemotypes, and suggested use as a reporter.

Thorne, N.Shen, M.Lea, W.A.Simeonov, A.Lovell, S.Auld, D.S.Inglese, J.

(2012) Chem Biol 19: 1060-1072

  • DOI: https://doi.org/10.1016/j.chembiol.2012.07.015
  • Primary Citation Related Structures: 
    4E5D

  • PubMed Abstract: 

    Firefly luciferase (FLuc) is frequently used as a reporter in high-throughput screening assays, owing to the exceptional sensitivity, dynamic range, and rapid measurement that bioluminescence affords. However, interaction of small molecules with FLuc has, to some extent, confounded its use in chemical biology and drug discovery. To identify and characterize chemotypes interacting with FLuc, we determined potency values for 360,864 compounds found in the NIH Molecular Libraries Small Molecule Repository, available in PubChem. FLuc inhibitory activity was observed for 12% of this library with discernible SAR. Characterization of 151 inhibitors demonstrated a variety of inhibition modes, including FLuc-catalyzed formation of multisubstrate adduct enzyme inhibitor complexes. As in some cell-based FLuc reporter assays, compounds acting as FLuc inhibitors yield paradoxical luminescence increases, thus data on compounds acquired from FLuc-dependent assays require careful analysis as described here.


  • Organizational Affiliation
    • National Center for Advancing Translational Sciences, Bethesda, MD 20892-3370, USA.

Macromolecule Content 

  • Total Structure Weight: 61.08 kDa 
  • Atom Count: 3,478 
  • Modeled Residue Count: 425 
  • Deposited Residue Count: 550 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Luciferin 4-monooxygenase550Photinus pyralisMutation(s): 0 
EC: 1.13.12.7
UniProt
Find proteins for P08659 (Photinus pyralis)
Explore P08659 
Go to UniProtKB:  P08659
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08659
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0NJ

Query on 0NJ



Download:Ideal Coordinates CCD File
B [auth A]2-(2-fluorophenyl)-6-methoxy-1,3-benzothiazole
C14 H10 F N O S
PPGLEUILAOUYQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.939α = 90
b = 83.939β = 90
c = 96.976γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-09-12
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description