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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.205 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.183 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.0 of the entry. See complete history


Literature

A new class of penicillin-binding protein inhibitors to address 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.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.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.12.27.630553
  • Primary Citation of Related Structures:  
    9MCZ, 9MD0

  • PubMed Abstract: 

    β-Lactams are the most widely used antibiotics for the treatment of bacterial infections because of their proven track record of safety and efficacy. However, susceptibility to β-lactam antibiotics is continually eroded by resistance mechanisms. Emerging multidrug-resistant (MDR) Neisseria gonorrhoeae strains possessing altered penA alleles (encoding PBP2) pose a global health emergency as they threaten the utility of ceftriaxone, the last remaining outpatient antibiotic. Here we disclose a novel benzoxaborinine-based penicillin-binding protein inhibitor series (boro-PBPi) that is envisioned to address penA- mediated resistance while offering protection against evolution and expansion of β-lactamases. Optimization of boro-PBPi led to the identification of compound 21 (VNRX-14079) that exhibits potent antibacterial activity against MDR N. gonorrhoeae achieved by high affinity binding to the PBP2 target. Boro-PBPi/PBP2 complex structures confirmed covalent interaction of the boron atom with Ser310 and the importance of the β 3 4 loop for improved affinity. 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 . 21 is a promising anti-gonorrhea agent poised for further advancement.


  • Organizational Affiliation

    Venatorx Pharmaceuticals, Inc., Malvern, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 2330Neisseria gonorrhoeae 35/02Mutation(s): 0 
Gene Names: penA
EC: 3.4.16.4
UniProt
Find proteins for Q8G8S8 (Neisseria gonorrhoeae)
Explore Q8G8S8 
Go to UniProtKB:  Q8G8S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8G8S8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BJC (Subject of Investigation/LOI)
Query on A1BJC

Download Ideal Coordinates CCD File 
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), 0.212 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.183 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.586α = 90
b = 60.735β = 90
c = 110.281γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
FFTphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1BJCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI141239

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release