9S5X | pdb_00009s5x

Crystal structure of Neisseria gonorrhoeae FabI in complex with NADH and (E)-3-((2R,3S)-3-hydroxy-2-methyl-4-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-b][1,4]diazepin-8-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide

• PDB DOI: https://doi.org/10.2210/pdb9S5X/pdb

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


• Deposited: 2025-07-30 Released: 2025-08-20 
• Deposition Author(s): Ronin, C., Gerusz, V., Ciesielski, F.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

The bactericidal FabI inhibitor Debio 1453 clears antibiotic-resistant Neisseria gonorrhoeae infection in vivo.

Gerusz, V., Regenass, P., Rousseau, Q., Moraine, V., Dao, J., Lave, X., Das, S., Hue Perron, J., Fajas Descamps, L., Bravo, J., Dieppois, G., Kaplan, N., Lefebre, M., Altomari, D., Romanov, V., Finn, T., Daram, P., Bernardini, F., Gross, M., Lysek, R., Adam, A., Pohin, D., Maio, M., Tatsis, V., Sunose, M., Ronin, C., Ciesielski, F., Ahlstrand, J., Jacobsson, S., Unemo, M., Cameron, D.R.

(2025) Nat Commun 16: 8309-8309

• PubMed: 40968127 
• DOI: https://doi.org/10.1038/s41467-025-63508-w
• Primary Citation of Related Structures:  
  9S5X


• PubMed Abstract: 
  

  Gonorrhoea is a prevalent sexually transmitted infection caused by the bacterial pathogen Neisseria gonorrhoeae. N. gonorrhoeae has demonstrated a remarkable capacity to evolve antibiotic resistance, with emerging strains that show resistance to all standard treatment options. The development of new antibiotics for gonorrhoea, especially those with novel targets and no pre-existing resistance, is critical. One such untapped antibacterial target in N. gonorrhoeae is FabI, an enoyl-acyl carrier protein reductase enzyme that is essential for fatty acid biosynthesis in this pathogen. In the current report, structure-based drug design using novel N. gonorrhoeae FabI inhibitor co-crystals guides medicinal chemistry toward increasing potency in the sub-nanomolar range and drives the discovery of Debio 1453. Debio 1453 is optimized for activity against N. gonorrhoeae and is highly active in vitro against diverse N. gonorrhoeae isolates including those resistant to the last remaining treatment options. Additionally, the compound presents a low propensity for selection of mutants with reduced susceptibility. Debio 1453 is efficacious in vivo against N. gonorrhoeae isolates with clinically relevant multi-drug resistance phenotypes in a murine vaginal gonorrhoea infection model underscoring Debio 1453 as a promising candidate for the treatment of gonorrhoea.

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Organizational Affiliation: 
• Debiopharm Research and Manufacturing SA, Martigny, Switzerland. [e-mail].
Debiopharm Research and Manufacturing SA, Martigny, Switzerland.
Debiopharm International SA, Lausanne, Switzerland.
Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology, University of Liverpool, Liverpool Health Partners, Liverpool, UK.
Nobelex Biotech, Inc., Toronto, ON, Canada.
Sygnature Discovery, Biocity, Nottingham, UK.
Novalix, Strasbourg, France.
WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
Institute for Global Health, University College London (UCL), London, UK.
Debiopharm International SA, Lausanne, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 62.29 kDa 
• Atom Count: 4,427 
• Modeled Residue Count: 515 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B	281	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names: NGO_1666 EC: 1.3.1.9
UniProt
Find proteins for Q5F696 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F696  Go to UniProtKB:  Q5F696

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
A1H1H (Subject of Investigation/LOI)	C [auth A], E [auth B]	(~{E})-~{N}-methyl-~{N}-[(3-methyl-1-benzofuran-2-yl)methyl]-3-[(2~{R},3~{S})-2-methyl-3-oxidanyl-4-oxidanylidene-1,2,3,5-tetrahydropyrido[2,3-b][1,4]diazepin-8-yl]prop-2-enamide C23 H24 N4 O4 YEFHSSWFLULRED-UGZSOSCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.26	α = 90
b = 91.26	β = 90
c = 241.06	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Ronin, C., Gerusz, V., Ciesielski, F.

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Funding Organization	Location	Grant Number
Other government	Switzerland	75A50122C00028

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Changes: Database references
• Version 1.2: 2025-10-01
  Changes: Database references