3LPG

Structure of E. coli beta-Glucuronidase bound with a novel, potent inhibitor 3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-((6-methyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)urea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Alleviating cancer drug toxicity by inhibiting a bacterial enzyme.

Wallace, B.D.Wang, H.Lane, K.T.Scott, J.E.Orans, J.Koo, J.S.Venkatesh, M.Jobin, C.Yeh, L.A.Mani, S.Redinbo, M.R.

(2010) Science 330: 831-835

  • DOI: https://doi.org/10.1126/science.1191175
  • Primary Citation of Related Structures:  
    3K46, 3K4A, 3K4D, 3LPF, 3LPG

  • PubMed Abstract: 

    The dose-limiting side effect of the common colon cancer chemotherapeutic CPT-11 is severe diarrhea caused by symbiotic bacterial β-glucuronidases that reactivate the drug in the gut. We sought to target these enzymes without killing the commensal bacteria essential for human health. Potent bacterial β-glucuronidase inhibitors were identified by high-throughput screening and shown to have no effect on the orthologous mammalian enzyme. Crystal structures established that selectivity was based on a loop unique to bacterial β-glucuronidases. Inhibitors were highly effective against the enzyme target in living aerobic and anaerobic bacteria, but did not kill the bacteria or harm mammalian cells. Finally, oral administration of an inhibitor protected mice from CPT-11-induced toxicity. Thus, drugs may be designed to inhibit undesirable enzyme activities in essential microbial symbiotes to enhance chemotherapeutic efficacy.


  • Organizational Affiliation

    Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucuronidase
A, B
605Escherichia coli K-12Mutation(s): 0 
Gene Names: b1617gurAgusAJW1609uidA
EC: 3.2.1.31
UniProt
Find proteins for P05804 (Escherichia coli (strain K12))
Explore P05804 
Go to UniProtKB:  P05804
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05804
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z78
Query on Z78

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-[(6-methyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl]urea
C20 H20 F N3 O3
IZEKTGGQNDYMPR-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
Z78 PDBBind:  3LPG Ki: 684 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.814α = 90
b = 76.934β = 124.75
c = 125.81γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
X-GENdata reduction
X-GENdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-22
    Changes: Data collection
  • Version 1.5: 2024-10-16
    Changes: Structure summary