9U9C

Crystal structure of NDM-1 in complex with hydrolyzed amoxicillin

This is a non-PDB format compatible entry.

Summary for 9U9C

• Entry DOI: 10.2210/pdb9u9c/pdb
• Descriptor: Metallo-beta-lactamase type 2, ZINC ION, (2~{R},4~{S})-2-[(1~{R})-1-[[(2~{R})-2-azanyl-2-(4-hydroxyphenyl)ethanoyl]amino]-2-oxidanyl-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid, ... (4 entities in total)
• Functional Keywords: hydrolase, ndm-1
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 2
• Total formula weight: 52357.52

Authors

Shi, X.,Zhang, Q.,Liu, W. (deposition date: 2025-03-27, release date: 2025-07-09, Last modification date: 2025-08-06)

Primary citation

Shi, X.,Yang, H.,Dai, Y.,Zhao, H.,Li, Y.,Li, Y.,Zhou, X.,Yan, H.,Zhang, Q.,Liu, W.
Crystal structure reveals the hydrophilic R1 group impairs NDM-1-ligand binding via water penetration at L3.
J Struct Biol X, 12:100133-100133, 2025

PubMed Abstract: The global spread of New Delhi metallo-β-lactamases (NDMs) has exacerbated the antimicrobial resistance crisis. This study resolved the crystal structure of NDM-1 hydrolyzing amoxicillin for the first time, revealed that the hydroxyl group in the R1 moiety of amoxicillin anchors a key water molecule (Wat1) via hydrogen bond, inducing a conformational shift in Met67 (average displacement of 3.8 Å compared to its position in complexes with ampicillin, penicillin G, and penicillin V) and impairing the hydrophobic interaction between the loop 3 and the substrate. Molecular dynamics simulations confirmed that the π-π stacking contact time between amoxicillin and the L3 critical residue Phe70 decreased to 4.3 % (ampicillin: 12.3 %), with a binding energy reduction of 10.5 kcal/mol. Steady-state kinetics showed that amoxicillin exhibited a 2.2-fold higher and a 5.2-fold higher compared to ampicillin, demonstrating that hydrophilic R1 groups impair enzyme-substrate binding. This work demonstrates the essential role of hydrophobic interactions in L3-mediated substrate binding and provides a novel strategy for designing L3-targeted NDM-1 inhibitors: maximize hydrophobicity and minimize polar surface area in the L3 contact region to block water penetration, thereby stabilizing the inhibitor-L3 interaction.

PubMed: 40687621
DOI: 10.1016/j.yjsbx.2025.100133

Experimental method

X-RAY DIFFRACTION (1.25 Å)