3BM6

AmpC beta-lactamase in complex with a p.carboxyphenylboronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors.

Tondi, D.Calo, S.Shoichet, B.K.Costi, M.P.

(2010) Bioorg Med Chem Lett 20: 3416-3419

  • DOI: 10.1016/j.bmcl.2010.04.007
  • Primary Citation of Related Structures:  
    3BM6

  • PubMed Abstract: 
  • A small set of boronic acids acting as low nanomolar inhibitors of AmpC beta-lactamase were designed and synthesized in the effort to improve affinity, pharmacokinetic properties, and to provide a valid lead compound. X-ray crystallography revealed the binary complex of the best inhibitor bound to the enzyme, highlighting possibilities for its further rational derivatization and chemical optimization ...

    A small set of boronic acids acting as low nanomolar inhibitors of AmpC beta-lactamase were designed and synthesized in the effort to improve affinity, pharmacokinetic properties, and to provide a valid lead compound. X-ray crystallography revealed the binary complex of the best inhibitor bound to the enzyme, highlighting possibilities for its further rational derivatization and chemical optimization.


    Organizational Affiliation

    Dipartimento di Scienze Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41126 Modena, Italy. tondid@unimore.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA, B358Escherichia coliMutation(s): 0 
Gene Names: ampCampA
EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12))
Explore P00811 
Go to UniProtKB:  P00811
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C9P (Subject of Investigation/LOI)
Query on C9P

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]4-(dihydroxyboranyl)-2-({[4-(phenylsulfonyl)thiophen-2-yl]sulfonyl}amino)benzoic acid
C17 H14 B N O8 S3
JJPKFZAOXOEFHQ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C9P PDBBind:  3BM6 Ki: 26 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.908α = 90
b = 77.18β = 115.98
c = 97.937γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2007-12-12 
  • Released Date: 2009-02-17 
  • Deposition Author(s): Tondi, D.

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description