9MAS | pdb_00009mas

Metal Beta Lactamase VIM-2 in Complex with Dual MBL/SBL Inhibitor 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.261 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural Optimization of Bicyclic Oxo-Boronates as Dual Metallo- and Serine-beta-Lactamase Inhibitors.

Yang, Z.B.Wei, S.Q.Wang, Y.G.Dong, X.M.Xu, H.X.Li, X.L.Peng, J.Yin, R.C.Li, G.B.

(2025) J Med Chem 68: 21807-21828

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02230
  • Primary Citation Related Structures: 
    9MAS, 9MB4

  • PubMed Abstract: 

    Gram-negative bacterial resistance to β-lactam antibiotics is a growing clinical problem, largely driven by the production of metallo-β-lactamases (MBLs) and serine-β-lactamases (SBLs). Developing dual inhibitors targeting both MBLs and SBLs has emerged as a focus in the fight against β-lactam resistance. We previously identified the bicyclic oxo-boronate CB1 as a dual MBL/SBL inhibitor through molecular generation based on the binding mode of carbapenem tetrahedral intermediates. Herein, we report the structural optimization of CB1 , yielding new bicyclic oxo-boronates with potent dual MBL/SBL inhibition, some of which could potentiate Meropenem efficacy against carbapenem-resistant Gram-negative superbugs. X-ray crystallography revealed a common binding mode of bicyclic oxo-boronates with VIM-2/NDM-1 MBL and OXA-48 SBL, mimicking the binding of carbapenem intermediates. YL6113 exhibited pharmacokinetic characteristics similar to Meropenem and manifested efficacy when combined with Meropenem in a murine sepsis model. This work provides the basis for developing oxo-boronate-based inhibitors targeting MBLs/SBLs and other relevant targets.


  • Organizational Affiliation
    • Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.

Macromolecule Content 

  • Total Structure Weight: 57.97 kDa 
  • Atom Count: 3,687 
  • Modeled Residue Count: 464 
  • Deposited Residue Count: 532 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase VIM-2
A, B
266Escherichia coliMutation(s): 0 
Gene Names: VIM-2blaVIM-2VIM2
EC: 3.5.2.6
UniProt
Find proteins for Q5U7L7 (Escherichia coli)
Explore Q5U7L7 
Go to UniProtKB:  Q5U7L7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5U7L7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ENM
(Subject of Investigation/LOI)

Query on A1ENM



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B]
9-[(4-methylpyrazol-1-yl)methyl]-3,3-bis(oxidanyl)-2,5-dioxa-3-boranuidabicyclo[4.4.0]deca-1(6),7,9-triene-10-carboxylic acid
C13 H14 B N2 O6
QNYKHWXDBHIASO-UHFFFAOYSA-N
ZN

Query on ZN



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.261 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.642α = 90
b = 80.073β = 90
c = 80.104γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing

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)China82473845, 82122065

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-11
    Type: Initial release