9F0S | pdb_00009f0s

VIM-2 in complex with GKV63 (5j) - dynamically chiral phosphonic acid-type metallo-beta-lactamase inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Dynamically chiral phosphonic acid-type metallo-beta-lactamase inhibitors.

Gulyas, K.V.Zhou, L.Salamonsen, D.Prester, A.Bartels, K.Bosman, R.Haffke, P.Li, J.Tamasi, V.Deufel, F.Thoma, J.Andersson Rasmussen, A.Csala, M.Schroder Leiros, H.K.Xu, Z.Widersten, M.Rohde, H.Schulz, E.C.Zhu, W.Erdelyi, M.

(2025) Commun Chem 8: 119-119

  • DOI: https://doi.org/10.1038/s42004-025-01510-5
  • Primary Citation of Related Structures:  
    9F0P, 9F0Q, 9F0R, 9F0S

  • PubMed Abstract: 

    Antibiotic resistance is a growing global health threat that risks the lives of millions. Among the resistance mechanisms, that mediated by metallo-β-lactamases is of particular concern as these bacterial enzymes dismantle most β-lactam antibiotics, which are our widest applied and cheapest to produce antibiotic agents. So far, no clinically applicable metallo-β-lactamase inhibitors are available. Aiming to adapt to structural variations, we introduce the inhibitor concept: dynamically chiral phosphonic acids. We demonstrate that they are straightforward to synthesize, penetrate bacterial membranes, inhibit the metallo-β-lactamase enzymes NDM-1, VIM-2 and GIM-1, and are non-toxic to human cells. Mimicking the transition state of β-lactam hydrolysis, they target the Zn ions of the metallo-β-lactamase active site. As a unique feature, both of their stereoisomers bind metallo-β-lactamases, which provides them unparalleled adaptability to the structural diversity of these enzymes, and may allow them to hamper bacteria's ability for resistance development.


  • Organizational Affiliation
    • Department of Chemistry - BMC, Organic Chemistry and the Uppsala Antibiotic Center; Uppsala University, Uppsala, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2
A, B
254Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM
EC: 3.5.2.6
UniProt
Find proteins for A0A0F7KYQ8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore A0A0F7KYQ8 
Go to UniProtKB:  A0A0F7KYQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F7KYQ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H8U (Subject of Investigation/LOI)
Query on A1H8U

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
[(~{R})-(2-hydroxyphenyl)-(2-thiophen-3-ylethanoylamino)methyl]phosphonic acid
C13 H14 N O5 P S
MGEYOJAOHCRYME-ZDUSSCGKSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
J [auth B],
K [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.506α = 90
b = 79.244β = 130.38
c = 67.716γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
autoPROCdata processing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany01KI2114
German Research Foundation (DFG)Germany458246365
Max Planck SocietyGermany--
Swedish Research CouncilSweden2013-8804
Uppsala Antibiotic CenterSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references