8YKS | pdb_00008yks

PaThiL in complex with AMP-PNP

PDB DOI: https://doi.org/10.2210/pdb8YKS/pdb
Entry: 8YKS supersedes: 7DU3

Classification: PROTEIN BINDING
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-05 Released: 2025-03-12
Deposition Author(s): Lin, J.Q., Chung, Z., Lescar, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.198 (Depositor), 0.199 (DCC)
R-Value Work:
0.182 (Depositor), 0.184 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A thiadiazolylidene-morpholine compound inhibits Pseudomonas aeruginosa by destabilizing the thiamine monophosphate kinase thiL.

Li, Y., Lin, J., Chung, Z., Yee Yeo, B.K., Lescar, J., Pethe, K.

(2026) J Biol Chem 302: 113112-113112

PubMed: 42103215 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2026.113112
Primary Citation Related Structures:
8YKS, 8YKU

PubMed Abstract:
Pseudomonas aeruginosa, an opportunistic gram-negative pathogen, poses a growing threat in healthcare-associated infections. Its intrinsic resistance and acquisition of carbapenemases have driven widespread multidrug resistance and severely limited treatment options. P. aeruginosa causes life-threatening infections including ventilator-associated pneumonia, bloodstream infections, complicated urinary tract infections, and chronic lung disease in cystic fibrosis. We identified and validated thiL, encoding thiamine monophosphate kinase, as a critical metabolic vulnerability and promising antibacterial target. ThiL deletion abolished virulence in murine lung and wound models and rendered bacteria incapable of survival without a supraphysiological level of thiamine pyrophosphate. A screen of 1231 kinase inhibitors identified VP3.15 as the first specific ThiL inhibitor with antibacterial potency. Mechanistic studies showed VP3.15 destabilizes ThiL, promoting protein unfolding and functional loss. These results establish ThiL as a druggable target and highlight metabolic dependencies as a therapeutic opportunity against multidrug-resistant P. aeruginosa.

Organizational Affiliation

Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.

Macromolecule Content

Total Structure Weight: 72.59 kDa
Atom Count: 5,145
Modeled Residue Count: 639
Deposited Residue Count: 688
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine-monophosphate kinase	A [auth B], B [auth A]	344	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: thiL, CAZ10_30480, DY930_26150, FDK04_05055, IPC116_27470, IPC1323_04495, IPC1509_03965, IPC582_16370, IPC620_29520, NCTC13621_06786 EC: 2.7.4.16
UniProt
Find proteins for Q9HWX7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HWX7 Go to UniProtKB: Q9HWX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HWX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain O [auth A] MOL2 format, chain H [auth B] MOL2 format, chain O [auth A] mmCIF format, chain H [auth B] mmCIF format, chain O [auth A]	H [auth B], O [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain H [auth B] Focus chain O [auth A] Interactions & Density Focus chain H [auth B] Focus chain O [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	C [auth B] D [auth B] E [auth B] J [auth A] K [auth A] C [auth B], D [auth B], E [auth B], J [auth A], K [auth A], L [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	F [auth B], G [auth B], M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain M [auth A] Focus chain N [auth A]