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Cryptic Binding Pockets in PDC‑3 β‑Lactamase Modulate Resistance Profiles.

Shuang Chen1, Fedaa Attana1,2, Andrea M Hujer3

  • 1UCL School of Pharmacy, London WC1N 1AX, U.K.

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|March 27, 2026
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Summary
This summary is machine-generated.

Researchers mapped protein conformational changes using deep learning. They discovered a hidden pocket in PDC-3 beta-lactamase, offering a new target for drug development to combat antibiotic resistance.

Keywords:
antibiotic resistancecryptic pocketdeep learningmolecular dynamicsβ-lactamase

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Cryptic binding pockets in proteins influence crucial functions like catalysis and allostery.
  • These pockets are often missed by experimental methods and standard molecular dynamics simulations.

Purpose of the Study:

  • To map the complete conformational landscape of the Ω-loop in class C β-lactamase PDC-3.
  • To identify novel cryptic pockets and understand their role in enzyme regulation and drug targeting.

Main Methods:

  • Integration of enhanced sampling techniques with an unsupervised deep-learning pipeline.
  • Analysis of protein conformational ensembles and molecular interactions.

Main Results:

  • Identified three distinct conformational states: crystal-like, expansive, and constricted.
  • Residues 219 and 221 function as molecular switches controlling enzyme states and resistance profiles.
  • Discovered a previously hidden cryptic pocket upon catalytic site occlusion, suggesting an allosteric target.

Conclusions:

  • The study presents a generalizable framework for uncovering hidden protein conformations and regulatory mechanisms.
  • The identified cryptic pocket in PDC-3 presents a novel allosteric target for developing inhibitors to combat antibiotic resistance.