7CJL

Metallo-Beta-Lactamase VIM-2 in complex with (S)-N-(3-(2H-tetrazol-5-yl)phenyl)-3-mercapto-2-methylpropanamide

PDB DOI: https://doi.org/10.2210/pdb7CJL/pdb

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

Deposited: 2020-07-11 Released: 2021-07-14
Deposition Author(s): Yan, Y.-H., Chen, J., Zhan, Z., Yu, Z.-J., Li, G., Li, G.-B., Guo, L., Wu, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.246
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of mercaptopropanamide-substituted aryl tetrazoles as new broad-spectrum metallo-beta-lactamase inhibitors.

Yan, Y.H., Chen, J., Zhan, Z., Yu, Z.J., Li, G., Guo, L., Li, G.B., Wu, Y., Zheng, Y.

(2020) RSC Adv 10: 31377-31384

PubMed: 35520685 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/d0ra06405j
Primary Citation of Related Structures:
7CJL

PubMed Abstract:
β-Lactam antibiotic resistance mediated by metallo-β-lactamases (MBL) has threatened global public health. There are currently no available inhibitors of MBLs for clinical use. We previously reported the ruthenium-catalyzed meta-selective C-H nitration synthesis method, leading to some meta -mercaptopropanamide substituted aryl tetrazoles as new potent MBL inhibitors. Here, we described the structure-activity relationship of meta - and ortho -mercaptopropanamide substituted aryl tetrazoles with clinically relevant MBLs. The resulting most potent compound 13a showed IC ₅₀ values of 0.044 μM, 0.396 μM and 0.71 μM against VIM-2, NDM-1 and IMP-1 MBL, respectively. Crystallographic analysis revealed that 13a chelated to active site zinc ions via the thiol group and interacted with the catalytically important residues Asn233 and Tyr67, providing further structural information for the development of thiol based MBL inhibitors.

Organizational Affiliation

Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Sichuan Engineering Laboratory for Plant-Sourced Drug, Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University Sichuan 610041 China yongxiangzheng@scu.edu.cn +86 199 3880 2868.

Macromolecule Content

Total Structure Weight: 50.19 kDa
Atom Count: 3,749
Modelled Residue Count: 462
Deposited Residue Count: 462
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase class B VIM-2	A [auth B], B [auth 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K2N0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G0O (Subject of Investigation/LOI) Query on G0O Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth A] MOL2 format, chain F [auth B] MOL2 format, chain I [auth A]	F [auth B], I [auth A]	(S)-N-(3-(2H-tetrazol-5-yl)phenyl)-3-mercapto-2-methylpropanamide C₁₁ H₁₃ N₅ O S ZUTCRKIDPCRTLZ-SSDOTTSWSA-N		Interactions Focus chain F [auth B] Focus chain I [auth A] Interactions & Density Focus chain F [auth B] Focus chain I [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	C [auth B], D [auth B], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain G [auth A] Focus chain H [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]