Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed ampicillin

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

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Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design.

Shi, X.Dai, Y.Lan, Z.Wang, S.Cui, L.Xiao, C.Zhao, K.Li, X.Liu, W.Zhang, Q.

(2024) Int J Biol Macromol 262: 130041-130041

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.130041
  • Primary Citation of Related Structures:  
    8GPC, 8GPD, 8GPE, 8I8F

  • PubMed Abstract: 

    Metallo-β-lactamases (MβLs) stand as significant resistant mechanism against β-lactam antibiotics in Gram-negative bacteria. The worldwide dissemination of New Delhi metallo-β-lactamases (NDMs) intensifies antimicrobial resistance, posing severe threats to human health due to the absence of inhibitors available in clinical therapy. L3, a flexible β-hairpin loop flanking the active site in MβLs, has been proven to wield influence over the reaction process by assuming a crucial role in substrate recognition and intermediate stabilization. In principle, it potentially retards product release from the enzyme, consequently reducing the overall turnover rate although the details regarding this aspect remain inadequately elucidated. In this study, we crystallized NDM-1 in complex with three penicillin substrates, conducted molecular dynamics simulations, and measured the steady-state kinetic parameters. These analyses consistently unveiled substantial disparities in their interactions with loop L3. We further synthesized a penicillin V derivative with increased hydrophobicity in the R1 side chain and co-crystallized it with NDM-1. Remarkably, this compound exhibited much stronger dynamic interplay with L3 during molecular dynamics simulation, showed much lower K m and k cat values, and demonstrated moderate inhibitory capacity to NDM-1 catalyzed meropenem hydrolysis. The data presented here may provide a strategic approach for designing mechanism-based MβL inhibitors focusing on structural elements external to the enzyme's active center.

  • Organizational Affiliation

    Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo beta lactamase NDM-1
A, B
270Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1bla NDM-1blaNDM1NDM-1
Find proteins for E9NWK5 (Klebsiella pneumoniae)
Explore E9NWK5 
Go to UniProtKB:  E9NWK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9NWK5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZZ7 (Subject of Investigation/LOI)
Query on ZZ7

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
(2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
C16 H21 N3 O5 S
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.26α = 90
b = 79.11β = 90
c = 134.35γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Database references