5MXQ

Crystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in Complex with ANT-90 Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5MXQ/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-24 Released: 2018-02-28 
• Deposition Author(s): Docquier, J.D., De Luca, F., Benvenuti, M., Di Pisa, F., Pozzi, C., Mangani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.227 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

SAR Studies Leading to the Identification of a Novel Series of Metallo-beta-lactamase Inhibitors for the Treatment of Carbapenem-Resistant Enterobacteriaceae Infections That Display Efficacy in an Animal Infection Model.

Leiris, S., Coelho, A., Castandet, J., Bayet, M., Lozano, C., Bougnon, J., Bousquet, J., Everett, M., Lemonnier, M., Sprynski, N., Zalacain, M., Pallin, T.D., Cramp, M.C., Jennings, N., Raphy, G., Jones, M.W., Pattipati, R., Shankar, B., Sivasubrahmanyam, R., Soodhagani, A.K., Juventhala, R.R., Pottabathini, N., Pothukanuri, S., Benvenuti, M., Pozzi, C., Mangani, S., De Luca, F., Cerboni, G., Docquier, J.D., Davies, D.T.

(2019) ACS Infect Dis 5: 131-140

• PubMed: 30427656 
• DOI: https://doi.org/10.1021/acsinfecdis.8b00246
• Primary Citation of Related Structures:  
  5MXQ, 5MXR, 6HF5


• PubMed Abstract: 
  

  The clinical effectiveness of carbapenem antibiotics such as meropenem is becoming increasingly compromised by the spread of both metallo-β-lactamase (MBL) and serine-β-lactamase (SBL) enzymes on mobile genetic elements, stimulating research to find new β-lactamase inhibitors to be used in conjunction with carbapenems and other β-lactam antibiotics. Herein, we describe our initial exploration of a novel chemical series of metallo-β-lactamase inhibitors, from concept to efficacy, in a survival model using an advanced tool compound (ANT431) in conjunction with meropenem.

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Organizational Affiliation: 

Antabio SAS , 436 rue Pierre et Marie Curie , 31670 Labège , France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.31 kDa 
• Atom Count: 1,872 
• Modelled Residue Count: 231 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase VIM-2	A	231	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, PAERUG_P32_London_17_VIM_2_10_11_06255
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0  Go to UniProtKB:  Q9K2N0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U8K	E [auth A]	3-(phenylsulfonylamino)pyridine-2-carboxylic acid C12 H10 N2 O4 S HOBWUTFQJLTDSS-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	G [auth A], H [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
U8K	Binding MOAD:  5MXQ	IC50: 1900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.227 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.909	α = 90
b = 77.9	β = 90
c = 79.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Docquier, J.D., De Luca, F., Benvenuti, M., Di Pisa, F., Pozzi, C., Mangani, S.

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Database references
• Version 1.2: 2019-04-24
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description