5MXQ | pdb_00005mxq

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.227 (Depositor), 0.231 (DCC)
R-Value Work:
0.176 (Depositor), 0.186 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsinfecdis.8b00246
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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 EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0 Go to UniProtKB: Q9K2N0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K2N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U8K Query on U8K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3-(phenylsulfonylamino)pyridine-2-carboxylic acid C₁₂ H₁₀ N₂ O₄ S HOBWUTFQJLTDSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.227 (Depositor), 0.231 (DCC)
R-Value Work: 0.176 (Depositor), 0.186 (DCC)
R-Value Observed: 0.179 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2025-10-01
Changes: Derived calculations, Structure summary