8CUP | pdb_00008cup

X-ray crystal structure of ADC-33 in complex with sulfonamidoboronic acid 6d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii .

Introvigne, M.L.Beardsley, T.J.Fernando, M.C.Leonard, D.A.Wallar, B.J.Rudin, S.D.Taracila, M.A.Rather, P.N.Colquhoun, J.M.Song, S.Fini, F.Hujer, K.M.Hujer, A.M.Prati, F.Powers, R.A.Bonomo, R.A.Caselli, E.

(2023) Antibiotics (Basel) 12

  • DOI: https://doi.org/10.3390/antibiotics12040644
  • Primary Citation Related Structures: 
    8CUL, 8CUM, 8CUO, 8CUP, 8CUQ

  • PubMed Abstract: 

    Acinetobacter baumannii is a Gram-negative organism listed as an urgent threat pathogen by the World Health Organization (WHO). Carbapenem-resistant A. baumannii (CRAB), especially, present therapeutic challenges due to complex mechanisms of resistance to β -lactams. One of the most important mechanisms is the production of β -lactamase enzymes capable of hydrolyzing β -lactam antibiotics. Co-expression of multiple classes of β -lactamases is present in CRAB; therefore, the design and synthesis of "cross-class" inhibitors is an important strategy to preserve the efficacy of currently available antibiotics. To identify new, nonclassical β -lactamase inhibitors, we previously identified a sulfonamidomethaneboronic acid CR167 active against Acinetobacter -derived class C β -lactamases (ADC-7). The compound demonstrated affinity for ADC-7 with a K i = 160 nM and proved to be able to decrease MIC values of ceftazidime and cefotaxime in different bacterial strains. Herein, we describe the activity of CR167 against other β -lactamases in A. baumannii : the cefepime-hydrolysing class C extended-spectrum β -lactamase (ESAC) ADC-33 and the carbapenem-hydrolyzing OXA-24/40 (class D). These investigations demonstrate CR167 as a valuable cross-class (C and D) inhibitor, and the paper describes our attempts to further improve its activity. Five chiral analogues of CR167 were rationally designed and synthesized. The structures of OXA-24/40 and ADC-33 in complex with CR167 and select chiral analogues were obtained. The structure activity relationships (SARs) are highlighted, offering insights into the main determinants for cross-class C/D inhibitors and impetus for novel drug design.


  • Organizational Affiliation
    • Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy.

Macromolecule Content 

  • Total Structure Weight: 82.39 kDa 
  • Atom Count: 6,365 
  • Modeled Residue Count: 718 
  • Deposited Residue Count: 724 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamaseA [auth B],
B [auth A]
362Acinetobacter baumanniiMutation(s): 0 
Gene Names: ampCBAA1790NC_1053EP550_05490EP560_12590EQH48_05445
EC: 3.5.2.6
UniProt
Find proteins for A7Y407 (Acinetobacter baumannii)
Explore A7Y407 
Go to UniProtKB:  A7Y407
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7Y407
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OZF
(Subject of Investigation/LOI)

Query on OZF



Download:Ideal Coordinates CCD File
C [auth B],
D [auth A]
3-[(4S)-4-ethyl-5,7,7-trihydroxy-2,2,7-trioxo-6-oxa-2lambda~6~-thia-3-aza-7lambda~5~-phospha-5-boraheptan-1-yl]benzoic acid
C11 H17 B N O9 P S
OKRPHJKYNCLTSY-SNVBAGLBSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.29α = 90
b = 83.82β = 90
c = 203.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI072219

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-05-01
    Changes: Database references
  • Version 1.3: 2024-11-06
    Changes: Structure summary