7CJL

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


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 

Starting Model: experimental
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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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase class B VIM-2A [auth B],
B [auth A]
231Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM-2bla vim-2bla-VIM-2blasVIM-2blaVIM2blmVIM-2PAERUG_P32_London_17_VIM_2_10_11_06255
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Explore Q9K2N0 
Go to UniProtKB:  Q9K2N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K2N0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G0O (Subject of Investigation/LOI)
Query on G0O

Download Ideal Coordinates CCD File 
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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B],
G [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
E [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.356α = 90
b = 90.132β = 90
c = 125.849γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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)China81874291
National Natural Science Foundation of China (NSFC)China81502989

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description