5W13

ADC-7 in complex with boronic acid transition state inhibitor SM23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of Acinetobacter-Derived Cephalosporinase: Exploring the Carboxylate Recognition Site Using Novel beta-Lactamase Inhibitors.

Caselli, E.Romagnoli, C.Powers, R.A.Taracila, M.A.Bouza, A.A.Swanson, H.C.Smolen, K.A.Fini, F.Wallar, B.J.Bonomo, R.A.Prati, F.

(2018) ACS Infect Dis 4: 337-348

  • DOI: 10.1021/acsinfecdis.7b00153
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Boronic acids are attracting a lot of attention as β-lactamase inhibitors, and in particular, compound S02030 ( K <sub>i </sub> = 44 nM) proved to be a good lead compound against ADC-7 ( Acinetobacter-derived cephalosporinase), one of the most signif ...

    Boronic acids are attracting a lot of attention as β-lactamase inhibitors, and in particular, compound S02030 ( K i = 44 nM) proved to be a good lead compound against ADC-7 ( Acinetobacter-derived cephalosporinase), one of the most significant resistance determinants in A. baumannii. The atomic structure of the ADC-7/S02030 complex highlighted the importance of critical structural determinants for recognition of the boronic acids. Herein, to elucidate the role in recognition of the R2-carboxylate, which mimics the C 3 /C 4 found in β-lactams, we designed, synthesized, and characterized six derivatives of S02030 (3a). Out of the six compounds, the best inhibitors proved to be those with an explicit negative charge (compounds 3a-c, 3h, and 3j, K i = 44-115 nM), which is in contrast to the derivatives where the negative charge is omitted, such as the amide derivative 3d ( K i = 224 nM) and the hydroxyamide derivative 3e ( K i = 155 nM). To develop a structural characterization of inhibitor binding in the active site, the X-ray crystal structures of ADC-7 in a complex with compounds 3c, SM23, and EC04 were determined. All three compounds share the same structural features as in S02030 but only differ in the carboxy-R2 side chain, thereby providing the opportunity of exploring the distinct binding mode of the negatively charged R2 side chain. This cephalosporinase demonstrates a high degree of versatility in recognition, employing different residues to directly interact with the carboxylate, thus suggesting the existence of a "carboxylate binding region" rather than a binding site in ADC enzymes. Furthermore, this class of compounds was tested against resistant clinical strains of A. baumannii and are effective at inhibiting bacterial growth in conjunction with a β-lactam antibiotic.


    Organizational Affiliation

    Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology and Microbiology , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States.,Department of Chemistry , Grand Valley State University , 1 Campus Drive , Allendale , Michigan 49401 , United States.,Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard , Cleveland , Ohio 44106 , United States.,Department of Life Sciences , University of Modena and Reggio Emilia , Via Campi 101 , 41125 , Modena , Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B, C, D
361Acinetobacter baumanniiMutation(s): 0 
EC: 3.5.2.6
Find proteins for Q6DRA1 (Acinetobacter baumannii)
Go to UniProtKB:  Q6DRA1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM2
Query on SM2

Download SDF File 
Download CCD File 
A, B, C, D
(1R)-1-(2-THIENYLACETYLAMINO)-1-(3-CARBOXYPHENYL)METHYLBORONIC ACID
C14 H14 B N O5 S
HQLQTGGLHBYZSA-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 88.712α = 90.00
b = 81.651β = 112.84
c = 106.415γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI072219

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Database references
  • Version 1.2: 2018-03-21
    Type: Database references