3FYZ

OXA-24 beta-lactamase complex with SA4-17 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase.

Bou, G.Santillana, E.Sheri, A.Beceiro, A.Sampson, J.M.Kalp, M.Bethel, C.R.Distler, A.M.Drawz, S.M.Pagadala, S.R.van den Akker, F.Bonomo, R.A.Romero, A.Buynak, J.D.

(2010) J Am Chem Soc 132: 13320-13331

  • DOI: https://doi.org/10.1021/ja104092z
  • Primary Citation of Related Structures:  
    3FV7, 3FYZ, 3FZC, 3G4P, 3MBZ

  • PubMed Abstract: 

    Class D β-lactamases represent a growing and diverse class of penicillin-inactivating enzymes that are usually resistant to commercial β-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa, novel β-lactamase inhibitors are urgently needed. Five unique 6-alkylidene-2'-substituted penicillanic acid sulfones (1-5) were synthesized and tested against OXA-24, a clinically important β-lactamase that inactivates carbapenems and is found in A. baumannii. Based upon the roles Tyr112 and Met223 play in the OXA-24 β-lactamase, we also engineered two variants (Tyr112Ala and Tyr112Ala,Met223Ala) to test the hypothesis that the hydrophobic tunnel formed by these residues influences inhibitor recognition. IC(50) values against OXA-24 and two OXA-24 β-lactamase variants ranged from 10 ± 1 (4 vs WT) to 338 ± 20 nM (5 vs Tyr112Ala, Met223Ala). Compound 4 possessed the lowest K(i) (500 ± 80 nM vs WT), and 1 possessed the highest inactivation efficiency (k(inact)/K(i) = 0.21 ± 0.02 μM(-1)  s(-1)). Electrospray ionization mass spectrometry revealed a single covalent adduct, suggesting the formation of an acyl-enzyme intermediate. X-ray structures of OXA-24 complexed to four inhibitors (2.0-2.6 Å) reveal the formation of stable bicyclic aromatic intermediates with their carbonyl oxygen in the oxyanion hole. These data provide the first structural evidence that 6-alkylidene-2'-substituted penicillin sulfones are effective mechanism-based inactivators of class D β-lactamases. Their unique chemistry makes them developmental candidates. Mechanisms for class D hydrolysis and inhibition are discussed, and a pathway for the evolution of the BlaR1 sensor of Staphylococcus aureus to the class D β-lactamases is proposed.


  • Organizational Affiliation

    Instituto de Investigación Biomédica de A Coruña (INIBIC), Complejo Hospitalario Universitario A Coruña, 15006-A Coruña, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase OXA-24244Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaOXA-33bla-OXA-40oxa-24oxa40
EC: 3.5.2.6
UniProt
Find proteins for Q8RLA6 (Acinetobacter baumannii)
Explore Q8RLA6 
Go to UniProtKB:  Q8RLA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RLA6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MXC
Query on MXC

Download Ideal Coordinates CCD File 
B [auth A](2S,3R)-2-[(7-aminocarbonyl-2-methanoyl-indolizin-3-yl)amino]-4-aminocarbonyloxy-3-methyl-3-sulfino-butanoic acid
C16 H18 N4 O8 S
WVRCRSIVCWLCEG-ZBEGNZNMSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
C [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
MXC PDBBind:  3FYZ Ki: 1600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.76α = 90
b = 102.76β = 90
c = 83.16γ = 90
Software Package:
Software NamePurpose
DNAdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-22
    Changes: Data collection