9H18 | pdb_00009h18

Crystal structure of OXA-405 in complex with nacubactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 
    0.199 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Electrostatic interactions influence diazabicyclooctane inhibitor potency against OXA-48-like beta-lactamases.

Hoff, J.F.Goudar, K.E.Calvopina, K.Beer, M.Hinchliffe, P.Shaw, J.M.Tooke, C.L.Takebayashi, Y.Cadzow, A.F.Harmer, N.J.Mulholland, A.J.Schofield, C.J.Spencer, J.

(2025) RSC Med Chem 

  • DOI: https://doi.org/10.1039/d5md00512d
  • Primary Citation of Related Structures:  
    9H11, 9H12, 9H13, 9H14, 9H15, 9H16, 9H17, 9H18, 9HPV

  • PubMed Abstract: 

    Carbapenemases, β-lactamases hydrolysing carbapenem antibiotics, challenge the treatment of multi-drug resistant bacteria. The OXA-48 carbapenemase is widely disseminated in Enterobacterales , necessitating new treatments for producer strains. Diazabicyclooctane (DBO) inhibitors, including avibactam and nacubactam, act on a wide range of enzymes to overcome β-lactamase-mediated resistance. Here we describe investigations on how avibactam and nacubactam inhibit OXA-48 and two variants, OXA-163 and OXA-405, with deletions in the β5-β6 loop neighbouring the active site that modify activity towards different β-lactam classes. Nacubactam is ∼80-fold less potent than avibactam towards OXA-48, but this difference reduces in OXA-163 and OXA-405. Crystal structures and molecular dynamics simulations reveal electrostatic repulsion between Arg214 on the OXA-48 β5-β6 active-site loop and nacubactam, but not avibactam; effects absent from simulations of OXA-163 and OXA-405, which lack Arg214. Crystallographic and mass spectrometry data demonstrate that all three enzymes support desulfation of the bound DBOs. The results indicate that interactions with Arg214 affect DBO potency, suggesting that sequence variation in OXA-48-like β-lactamases affects reactivity towards inhibitors as well as β-lactam substrates.


  • Organizational Affiliation
    • School of Cellular and Molecular Medicine, University of Bristol Bristol BS8 1TD UK Jim.Spencer@bristol.ac.uk.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
241Serratia marcescensMutation(s): 0 
Gene Names: blaOXA-405
EC: 3.5.2.6
UniProt
Find proteins for A0A0F6P2I5 (Serratia marcescens)
Explore A0A0F6P2I5 
Go to UniProtKB:  A0A0F6P2I5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F6P2I5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
I [auth A]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
OP0 (Subject of Investigation/LOI)
Query on OP0

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
(2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C9 H18 N4 O7 S
YTAWXXHGLPATIN-SFYZADRCSA-N
A1IYS (Subject of Investigation/LOI)
Query on A1IYS

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
(2S,5R)-N-(2-azanylethoxy)-1-methanoyl-5-(oxidanylamino)piperidine-2-carboxamide
C9 H18 N4 O4
SGDIINYEFNSHTO-SFYZADRCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free:  0.199 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.692α = 90
b = 123.692β = 90
c = 159.347γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomR102376-101

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references