4GEE

Pyrrolopyrimidine inhibitors of DNA gyrase B and topoisomerase IV, part I: structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.

Structural Biology Knowledgebase: 4GEE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GEE

Classification: Isomerase / Isomerase inhibitor

Total Structure Weight: 24299.73

Macromolecule Entities
Molecule Chains Length Organism Details
DNA gyrase subunit B A 215 Enterococcus faecalis EC#: 5.99.1.3 IUBMB
Gene Name(s): gyrB EF_0005

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0WT
Query on 0WT

A (1R,5S,6s)-3-[5-chloro-6-ethyl-2-(pyrimidin- 5-yloxy)-7H-pyrrolo[2,3-d]pyrimidin-4-yl]- 3-azabicyclo[3.1.0]hexan-6-amine
C17 H18 Cl N7 O
YZRGALHCPBRTES-MSRIBSCDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0WT N/A in BindingDB
Ki: 1 nM  BindingMOAD
Ki: 1 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.171
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.93 α = 90.00
b = 58.08 β = 90.00
c = 66.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-01
  • Released Date: 2013-02-13
  • Deposition author(s): Bensen, D.C., Chen, Z., Tari, L.W.

Revision History

  • 2013-02-27
    Type: Citation | Details: Citation update