5Y6E | pdb_00005y6e

VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.173 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 
    0.138 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

((S)-3-Mercapto-2-methylpropanamido)acetic acid derivatives as metallo-beta-lactamase inhibitors: Synthesis, kinetic and crystallographic studies.

Liu, S.Jing, L.Yu, Z.-J.Wu, C.Zheng, Y.Zhang, E.Chen, Q.Yu, Y.Guo, L.Wu, Y.Li, G.-B.

(2018) Eur J Med Chem 145: 649-660

  • DOI: https://doi.org/10.1016/j.ejmech.2018.01.032
  • Primary Citation Related Structures: 
    5Y6D, 5Y6E

  • PubMed Abstract: 

    The emergence and global spread of metallo-β-lactamase (MBL) mediated resistance to almost all β-lactam antibacterials poses a serious threat to public health. Since no clinically useful MBL inhibitors have been reported, there is an urgent need to develop new potent broad-spectrum MBL inhibitors effective against antibacterial resistance. Herein, we synthesized a set of 2-substituted ((S)-3-mercapto-2-methylpropanamido) acetic acid derivatives, some of which displayed potent inhibition with high ligand efficiency to the clinically relevant MBL subtypes, Verona Integron-encoded MBL (VIM)-2 and New Delhi MBL (NDM)-1. Kinetic studies revealed that the inhibitors are not strong zinc chelators in solution, and they bind reversibly to VIM-2 but dissociate very slowly. Crystallographic analyses revealed that they inhibit VIM-2 via chelating the active site zinc ions and interacting with catalytically important residues. Further cell- and zebrafish-based assays revealed that the inhibitors slightly increase susceptibility of E. coli cells expressing VIM-2 to meropenem, and they have no apparent toxicity to the viability of HEK293T cells and the zebrafish embryogenesis.


  • Organizational Affiliation
    • Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China.

Macromolecule Content 

  • Total Structure Weight: 50.47 kDa 
  • Atom Count: 3,990 
  • Modeled Residue Count: 462 
  • Deposited Residue Count: 462 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase class B VIM-2
A, B
231Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM-2bla vim-2bla-VIM-2blasVIM-2blaVIM2blmVIM-2PAERUG_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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K2N0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8PO

Query on 8PO



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
(2R)-2-(4-hydroxyphenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic acid
C12 H15 N O4 S
XFVAHOYBWXJSDW-GMSGAONNSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
I [auth B]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
M [auth B],
N [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.173 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 0.138 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.355α = 90
b = 74.452β = 129.46
c = 64.456γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2018-01-24 
  • Deposition Author(s): Li, G.-B.

Funding OrganizationLocationGrant Number
NSFCChina81502989

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-02-07
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description