2R9W

AmpC beta-lactamase with bound Phthalamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.

Babaoglu, K.Simeonov, A.Irwin, J.J.Nelson, M.E.Feng, B.Thomas, C.J.Cancian, L.Costi, M.P.Maltby, D.A.Jadhav, A.Inglese, J.Austin, C.P.Shoichet, B.K.

(2008) J.Med.Chem. 51: 2502-2511

  • DOI: 10.1021/jm701500e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • High-throughput screening (HTS) is widely used in drug discovery. Especially for screens of unbiased libraries, false positives can dominate "hit lists"; their origins are much debated. Here we determine the mechanism of every active hit from a scree ...

    High-throughput screening (HTS) is widely used in drug discovery. Especially for screens of unbiased libraries, false positives can dominate "hit lists"; their origins are much debated. Here we determine the mechanism of every active hit from a screen of 70,563 unbiased molecules against beta-lactamase using quantitative HTS (qHTS). Of the 1,274 initial inhibitors, 95% were detergent-sensitive and were classified as aggregators. Among the 70 remaining were 25 potent, covalent-acting beta-lactams. Mass spectra, counter-screens, and crystallography identified 12 as promiscuous covalent inhibitors. The remaining 33 were either aggregators or irreproducible. No specific reversible inhibitors were found. We turned to molecular docking to prioritize molecules from the same library for testing at higher concentrations. Of 16 tested, 2 were modest inhibitors. Subsequent X-ray structures corresponded to the docking prediction. Analog synthesis improved affinity to 8 microM. These results suggest that it may be the physical behavior of organic molecules, not their reactivity, that accounts for most screening artifacts. Structure-based methods may prioritize weak-but-novel chemotypes in unbiased library screens.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2330, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
358Escherichia coli (strain K12)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, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
23C
Query on 23C

Download SDF File 
Download CCD File 
A, B
2-[(1R)-1-carboxy-2-naphthalen-1-ylethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid
C22 H15 N O6
CZNPWASYMRBJCX-GOSISDBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
23CKi: 5000 nM (100) BINDINGDB
23CKi: 8000 nM BINDINGMOAD
23CKi: 8000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.683α = 90.00
b = 77.255β = 116.53
c = 97.939γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACphasing
REFMACrefinement
Blu-Icedata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description