4LV3

AmpC beta-lactamase in complex with (3,5-di-tert-butylphenyl) boronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Covalent docking of large libraries for the discovery of chemical probes.

London, N.Miller, R.M.Krishnan, S.Uchida, K.Irwin, J.J.Eidam, O.Gibold, L.Cimermancic, P.Bonnet, R.Shoichet, B.K.Taunton, J.

(2014) Nat.Chem.Biol. 10: 1066-1072

  • DOI: 10.1038/nchembio.1666
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaig ...

    Chemical probes that form a covalent bond with a protein target often show enhanced selectivity, potency and utility for biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Here we describe a general method (DOCKovalent) for screening large virtual libraries of electrophilic small molecules. We apply this method prospectively to discover reversible covalent fragments that target distinct protein nucleophiles, including the catalytic serine of AmpC β-lactamase and noncatalytic cysteines in RSK2, MSK1 and JAK3 kinases. We identify submicromolar to low-nanomolar hits with high ligand efficiency, cellular activity and selectivity, including what are to our knowledge the first reported reversible covalent inhibitors of JAK3. Crystal structures of inhibitor complexes with AmpC and RSK2 confirm the docking predictions and guide further optimization. As covalent virtual screening may have broad utility for the rapid discovery of chemical probes, we have made the method freely available through an automated web server (http://covalent.docking.org/).


    Organizational Affiliation

    1] Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA. [2] Howard Hughes Medical Institute, University of California-San Francisco, San Francisco, California, USA.,Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, California, USA.,1] Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA. [2] Faculty of Pharmacy, University of Toronto, Toronto, Canada. [3] Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada.,1] Clermont Université, UMR 1071 INSERM-Université d'Auvergne, Clermont-Ferrand, France. [2] INRA, USC 2018, Clermont-Ferrand, France. [3] Service de Bactériologie, Centre Hospitalier Universitaire, Clermont-Ferrand, France.,1] Faculty of Pharmacy, University of Toronto, Toronto, Canada. [2] Ontario Institute for Cancer Research, University of Toronto, Toronto, Canada. [3] Clermont Université, UMR 1071 INSERM-Université d'Auvergne, Clermont-Ferrand, France.,Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California, USA.,Chemistry and Chemical Biology Graduate Program, University of California-San Francisco, San Francisco, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
358Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ampC (ampA)
EC: 3.5.2.6
Find proteins for P00811 (Escherichia coli (strain K12))
Go to UniProtKB:  P00811
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
25N
Query on 25N

Download SDF File 
Download CCD File 
A, B
(3,5-di-tert-butylphenyl)boronic acid
C14 H23 B O2
RPCBIEHUQSGPNA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.550α = 90.00
b = 76.790β = 115.72
c = 98.080γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-11-05
    Type: Database references
  • Version 1.2: 2014-11-26
    Type: Database references