4KZA

Crystal structure of AmpC beta-lactamase in complex with fragment 48 (3-(cyclopropylsulfamoyl)thiophene-2-carboxylic acid)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Increasing chemical space coverage by combining empirical and computational fragment screens.

Barelier, S.Eidam, O.Fish, I.Hollander, J.Figaroa, F.Nachane, R.Irwin, J.J.Shoichet, B.K.Siegal, G.

(2014) Acs Chem.Biol. 9: 1528-1535

  • DOI: 10.1021/cb5001636
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverag ...

    Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco , 1700 4th St., Byers Hall, San Francisco, California 94158, United States.




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
NZ9
Query on NZ9

Download SDF File 
Download CCD File 
A, B
3-(cyclopropylsulfamoyl)thiophene-2-carboxylic acid
C8 H9 N O4 S2
LMYZTCQLGNOUQX-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NZ9Ki: 200000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.620α = 90.00
b = 76.630β = 116.91
c = 97.980γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references