9R8F | pdb_00009r8f

CTX-M-14 complexes with 3D Boron Heterocycles synthetized via EnT Catalysis

• PDB DOI: https://doi.org/10.2210/pdb9R8F/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-16 Released: 2026-03-25 
• Deposition Author(s): Perbandt, M., Molloy, J.J., Oberthuer, D.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.214 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Fused 3D boron heterocycles via EnT catalysis: synthesis, modification and validation as beta-lactamase inhibitors.

Kortman, H.M., Fang, H., Bastick, K.A.C., Volkel, C., Oberthur, D., Seeberger, P.H., Perbandt, M., Molloy, J.J.

(2026) Chem Sci 17: 247-254

• PubMed: 41221109 
• DOI: https://doi.org/10.1039/d5sc05518k
• Primary Citation Related Structures: 
  9R8F


• PubMed Abstract: 
  

  The installation of a boron unit into bioactive scaffolds continues to unlock novel modes of molecular recognition in drug discovery. As such, de novo strategies to access 3D boron-containing frameworks, that modulate the intrinsic reactivity at boron, are being intensively pursued. Herein, we report a visible light-mediated energy transfer (EnT) catalysis strategy that enables the [2 + 2] cycloaddition of boron-containing heterocycles to construct 3D frameworks with high structural complexity. Leveraging both inter- and intramolecular cycloadditions, a suite of angularly fused boron heterocycles was accessed, offering enhanced steric shielding and modular handles for additional interactions. A boron deletion strategy permits the synthesis of benzofuran scaffolds, otherwise inaccessible via direct EnT. Crucially, the resulting 3D architectures mimic structural motifs found in the potent β-lactamase inhibitor Xeruborbactam. The biological relevance of these frameworks was validated by NMR titration, p K _a analysis, and co-crystallisation with serine β-lactamase CTX-M-14, revealing enantiospecific binding and a well-defined hydrogen bonding network. These results establish a versatile platform for the synthesis of functionalised boron heterocycles with direct translational potential in medicinal chemistry.

---

Organizational Affiliation: 
• Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany [e-mail].
Department of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany.
Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY Notkestr. 85 22607 Hamburg Germany.
Department of Chemistry, Institute for Physical Chemistry, University of Hamburg Grindelallee 117 20146 Hamburg Germany [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 28.11 kDa 
• Atom Count: 2,239 
• Modeled Residue Count: 262 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	262	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: ctx-m-14 EC: 3.5.2.6
UniProt
Find proteins for D2D9A0 (Klebsiella pneumoniae) Explore D2D9A0  Go to UniProtKB:  D2D9A0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JDI (Subject of Investigation/LOI)	B [auth A]	(1~{R},2~{a}~{R},8~{b}~{R})-8-fluoranyl-3-oxidanyl-1,2,2~{a},8~{b}-tetrahydrocyclobuta[c][1,2]benzoxaborinine-1-carbonitrile C11 H9 B F N O2 HJELYBQKKZFUDV-PJKMHFRUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.214 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.54	α = 90
b = 41.54	β = 90
c = 231.3	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Perbandt, M., Molloy, J.J., Oberthuer, D.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release