1Q2Q

Enterobacter cloacae GC1 class C beta-lactamase complexed with penem WAY185229


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-activity relationship of 6-methylidene penems bearing tricyclic heterocycles as broad-spectrum beta-lactamase inhibitors: crystallographic structures show unexpected binding of 1,4-thiazepine intermediates

Venkatesan, A.M.Gu, Y.Dos Santos, O.Abe, T.Agarwal, A.Yang, Y.Petersen, P.J.Weiss, W.J.Mansour, T.S.Nukaga, M.Hujer, A.Bonomo, R.A.Knox, J.R.

(2004) J.Med.Chem. 47: 6556-6568

  • DOI: 10.1021/jm049680x
  • Primary Citation of Related Structures:  1Q2P

  • PubMed Abstract: 
  • The design and synthesis of a series of seven tricyclic 6-methylidene penems as novel class A and C serine beta-lactamase inhibitors is described. These compounds proved to be very potent inhibitors of the TEM-1 and AmpC beta-lactamases and less so a ...

    The design and synthesis of a series of seven tricyclic 6-methylidene penems as novel class A and C serine beta-lactamase inhibitors is described. These compounds proved to be very potent inhibitors of the TEM-1 and AmpC beta-lactamases and less so against the class B metallo-beta-lactamase CcrA. In combination with piperacillin, their in vitro activities enhanced susceptibility of all class C resistant strains from various bacteria. Crystallographic structures of a serine-bound reaction intermediate of 17 with the class A SHV-1 and class C GC1 enzymes have been established to resolutions of 2.0 and 1.4 A, respectively, and refined to R-factors equal 0.163 and 0.145. In both beta-lactamases, a seven-membered 1,4-thiazepine ring has formed. The stereogenic C7 atom in the ring has the R configuration in the SHV-1 intermediate and has both R and S configurations in the GC1 intermediate. Hydrophobic stacking interactions between the tricyclic C7 substituent and a tyrosine side chain, rather than electrostatic or hydrogen bonding by the C3 carboxylic acid group, dominate in both complexes. The formation of the 1,4- thiazepine ring structures is proposed based on a 7-endo-trig cyclization.


    Organizational Affiliation

    Wyeth Research, 401 N. Middletown Road, Pearl River, New York 10965, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
class C beta-lactamase
A
363Enterobacter cloacaeEC: 3.5.2.6
Find proteins for Q59401 (Enterobacter cloacae)
Go to UniProtKB:  Q59401
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WY2
Query on WY2

Download SDF File 
Download CCD File 
A
(6,7-DIHYDRO-5H-CYCLOPENTA[D]IMIDAZO[2,1-B]THIAZOL-2-YL]-4,7-DIHYDRO[1,4]THIAZEPINE-3,6-DICARBOXYLIC ACID
C15 H13 N3 O4 S2
CHNMLWCTGYMVFH-GFCCVEGCSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 76.223α = 90.00
b = 69.046β = 90.00
c = 62.152γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model