9C81

X-ray crystal structure of AmpC beta-lactamase with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 

Starting Model: experimental
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Literature

The impact of library size and scale of testing on virtual screening.

Liu, F.Mailhot, O.Glenn, I.S.Vigneron, S.F.Bassim, V.Xu, X.Fonseca-Valencia, K.Smith, M.S.Radchenko, D.S.Fraser, J.S.Moroz, Y.S.Irwin, J.J.Shoichet, B.K.

(2025) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-024-01797-w
  • Primary Citation of Related Structures:  
    9C6P, 9C81, 9C84, 9DHL

  • PubMed Abstract: 

    Virtual ligand libraries for ligand discovery have recently increased 10,000-fold. Whether this has improved hit rates and potencies has not been directly tested. Meanwhile, typically only dozens of docking hits are assayed, clouding hit-rate interpretation. Here we docked a 1.7 billion-molecule virtual library against β-lactamase, testing 1,521 new molecules and comparing the results to a 99 million-molecule screen where 44 molecules were tested. In a larger screen, hit rates improved twofold, more scaffolds were discovered and potency improved. Fifty-fold more inhibitors were found, supporting the idea that the large libraries harbor many more ligands than are being tested. In sampling smaller sets from the 1,521, hit rates only converged when several hundred molecules were tested. Hit rates and affinities improved steadily with docking score. It may be that as the scale of docking libraries and their testing grows, both ligands and our ability to rank them will improve.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AmpC Beta-lactamase
A, B
377Escherichia coliMutation(s): 0 
Gene Names: ampCampAb4150JW4111
EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12))
Explore P00811 
Go to UniProtKB:  P00811
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00811
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AU0 (Subject of Investigation/LOI)
Query on A1AU0

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2R)-2-phenoxy-3-{[(1S,2S,4S)-spiro[bicyclo[2.2.1]heptane-7,1'-cyclopropane]-2-carbonyl]amino}propanoic acid
C19 H23 N O4
MJMYSNTUGIKOIH-WWTUQBGBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.03α = 90
b = 78.17β = 115.48
c = 97.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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 General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Database references, Structure summary