6DTE

GlcNAc-inspired cyclophellitol bound to NagZ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to beta-lactams in Pseudomonas aeruginosa.

Ho, L.A.Winogrodzki, J.L.Debowski, A.W.Madden, Z.Vocadlo, D.J.Mark, B.L.Stubbs, K.A.

(2018) Chem Commun (Camb) 54: 10630-10633

  • DOI: 10.1039/c8cc05281f
  • Primary Citation of Related Structures:  
    6DTE

  • PubMed Abstract: 
  • The development of a potent mechanism-based inactivator of NagZ, an enzyme critical to the production of inducible AmpC β-lactamase in Gram-negative bacteria, is presented. This inactivator significantly reduces MIC values for important β-lactams against a clinically relevant strain of Pseudomonas aeruginosa ...

    The development of a potent mechanism-based inactivator of NagZ, an enzyme critical to the production of inducible AmpC β-lactamase in Gram-negative bacteria, is presented. This inactivator significantly reduces MIC values for important β-lactams against a clinically relevant strain of Pseudomonas aeruginosa.


    Organizational Affiliation

    School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia. keith.stubbs@uwa.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hexosaminidaseA, B350Burkholderia cenocepaciaMutation(s): 0 
Gene Names: 
EC: 3.2.1.52
UniProt
Find proteins for A0A125HFC0 (Burkholderia cenocepacia)
Explore A0A125HFC0 
Go to UniProtKB:  A0A125HFC0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H9J (Subject of Investigation/LOI)
Query on H9J

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2,2,2-trifluoro-N-[(1R,2R,3R,4R,5R,6R)-2,3,5,6-tetrahydroxy-4-(hydroxymethyl)cyclohexyl]acetamide
C9 H14 F3 N O6
RPAYCNWWSJECNN-ZGGPPPIHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.91α = 90
b = 88.14β = 92.03
c = 67.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada201603PJT-361930

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence