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 


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
Expand
  • 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]
D [auth B],
E [auth B],
F [auth B],
G [auth B],
I [auth A],
J [auth A],
K [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 


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