8AXP | pdb_00008axp

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

PDB DOI: https://doi.org/10.2210/pdb8AXP/pdb

Classification: HYDROLASE
Organism(s): Neisseria gonorrhoeae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-31 Released: 2022-11-09
Deposition Author(s): Roe, S.M., Fearon, D.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.364 (Depositor), 0.375 (DCC)
R-Value Work:
0.335 (Depositor), 0.346 (DCC)
R-Value Observed:
0.336 (Depositor)

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

PubMed: 36265082 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.orglett.2c02996
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 44.1 kDa
Atom Count: 3,324
Modeled Residue Count: 380
Deposited Residue Count: 384
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A [auth B], B [auth A]	192	Neisseria gonorrhoeae	Mutation(s): 0 Gene Names: pth, NGK_0538 EC: 3.1.1.29
UniProt
Find proteins for B4RK78 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RK78 Go to UniProtKB: B4RK78
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4RK78
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O0J (Subject of Investigation/LOI) Query on O0J Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain H [auth A] MOL2 format, chain C [auth B] MOL2 format, chain H [auth A] mmCIF format, chain C [auth B] mmCIF format, chain H [auth A]	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		Interactions Focus chain C [auth B] Focus chain H [auth A] Interactions & Density Focus chain C [auth B] Focus chain H [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	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		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]