RCSB PDB - 8AXP: Neisseria gonorrhoeae peptidyl-tRNA hydrolase complexed with an XChem hit.

 8AXP

Neisseria gonorrhoeae peptidyl-tRNA hydrolase complexed with an XChem hit.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.364 
  • R-Value Work: 0.335 
  • R-Value Observed: 0.336 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Synthesis of a Thiazole Library via an Iridium-Catalyzed Sulfur Ylide Insertion Reaction.

Hassell-Hart, S.Speranzini, E.Srikwanjai, S.Hossack, E.Roe, S.M.Fearon, D.Akinbosede, D.Hare, S.Spencer, J.

(2022) Org Lett 24: 7924-7927

  • DOI: https://doi.org/10.1021/acs.orglett.2c02996
  • Primary Citation of Related Structures:  
    8AXP

  • PubMed Abstract: 

    A library of thiazoles and selenothiazoles were synthesized via Ir-catalyzed ylide insertion chemistry. This process is a functional group, particularly heterocycle-substituent tolerant. This was applied to the synthesis of fanetizole, an anti-inflammatory drug, and a thiazole-containing drug fragment that binds to the peptidyl-tRNA hydrolase (Pth) in Neisseria gonorrheae bacteria.


  • Organizational Affiliation

    Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolaseA [auth B],
B [auth A]
192Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: pthNGK_0538
EC: 3.1.1.29
UniProt
Find proteins for B4RK78 (Neisseria gonorrhoeae (strain NCCP11945))
Explore B4RK78 
Go to UniProtKB:  B4RK78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4RK78
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O0J (Subject of Investigation/LOI)
Query on O0J

Download Ideal Coordinates CCD File 
C [auth B],
H [auth A]
N-[4-(2-amino-1,3-thiazol-4-yl)phenyl]acetamide
C11 H11 N3 O S
VBBNSESFUHRMJU-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth B]
E [auth B]
F [auth B]
G [auth B]
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.364 
  • R-Value Work: 0.335 
  • R-Value Observed: 0.336 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.44α = 90
b = 71.51β = 90
c = 146.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted O0JClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description