9MCZ | pdb_00009mcz

Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02 in complex with boronate inhibitor VNRX-6884

• PDB DOI: https://doi.org/10.2210/pdb9MCZ/pdb

• Classification: LIGASE
• Organism(s): Neisseria gonorrhoeae 35/02
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-05 Released: 2025-01-22 
• Deposition Author(s): Stratton, C.M., Bala, S., Davies, C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.205 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

A penicillin-binding protein inhibitor series to target drug-resistant Neisseria gonorrhoeae.

Uehara, T., Zulli, A.L., Miller, B., Avery, L.M., Boyd, S.A., Chatwin, C.L., Chu, G.H., Drager, A.S., Edwards, M., Emeigh Hart, S.G., Line, N.J., Myers, C.L., Rongala, G., Stevenson, A., Uehara, K., Yi, F., Wang, B., Liu, Z., Wang, M., Zhao, Z., Zhou, X., Zhao, H., Stratton, C.M., Bala, S., Davies, C., Tkavc, R., Jerse, A.E., Pevear, D.C., Burns, C.J., Daigle, D.M., Condon, S.M.

(2026) Nat Microbiol 

• PubMed: 41951974 
• DOI: https://doi.org/10.1038/s41564-026-02309-3
• Primary Citation Related Structures: 
  9MCZ, 9MD0, 9Z5T


• PubMed Abstract: 
  

  Emerging multidrug-resistant Neisseria gonorrhoeae strains possessing altered penA alleles (encoding penicillin-binding protein 2, PBP2) threaten the utility of ceftriaxone, the last remaining outpatient antibiotic for gonorrhoea treatment, posing a global health emergency. Here we report a benzoxaborinine-based penicillin-binding protein inhibitor series (boro-PBPi) developed to address penA-mediated ceftriaxone resistance. Optimization of boro-PBPi led to the identification of compound 21 (VNRX-14079), which exhibited potent antibacterial activity against multidrug-resistant N. gonorrhoeae through high-affinity binding to the PBP2 target. Boro-PBPi-PBP2 complex structures confirmed the covalent interaction of the boron atom with the catalytic residue Ser310 and the importance of the β ₃ -β ₄ loop mobility for improved affinity. Boro-PBPi 21 elicits bactericidal activity, a low frequency of resistance, a good safety profile, suitable pharmacokinetic properties and in vivo efficacy in a murine infection model against ceftriaxone-resistant N. gonorrhoeae. Boro-PBPi 21 is therefore a promising antigonorrhoea agent poised for further advancement.

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Organizational Affiliation: 
• Venatorx Pharmaceuticals, Inc., Malvern, PA, USA. [e-mail].
Venatorx Pharmaceuticals, Inc., Malvern, PA, USA.
BioDuro-Sundia, Beijing, China.
Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, USA.
Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
Spring Mill Pharma Inc., Malvern, PA, USA.
Venatorx Pharmaceuticals, Inc., Malvern, PA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.92 kDa 
• Atom Count: 2,634 
• Modeled Residue Count: 324 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 2	A	330	Neisseria gonorrhoeae 35/02	Mutation(s): 0  Gene Names: penA EC: 3.4.16.4
UniProt
Find proteins for Q8G8S8 (Neisseria gonorrhoeae) Explore Q8G8S8  Go to UniProtKB:  Q8G8S8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BJC (Subject of Investigation/LOI)	B [auth A]	(3R)-3-{[(2R)-2-[(4-ethyl-2,3-dioxopiperazine-1-carbonyl)amino]-2-(4-phosphonophenyl)acetyl]amino}-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid C24 H26 B N4 O11 P XZMSMKVMMWSBQP-ZWKOTPCHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.205 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.586	α = 90
b = 60.735	β = 90
c = 110.281	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
FFT	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Stratton, C.M., Bala, S., Davies, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI141239

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release
  
• Version 1.1: 2026-04-22
  Changes: Database references