4KPZ

Hin GlmU bound to a small molecule fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational design of inhibitors of the bacterial cell wall synthetic enzyme GlmU using virtual screening and lead-hopping.

Doig, P.Boriack-Sjodin, P.A.Dumas, J.Hu, J.Itoh, K.Johnson, K.Kazmirski, S.Kinoshita, T.Kuroda, S.Sato, T.O.Sugimoto, K.Tohyama, K.Aoi, H.Wakamatsu, K.Wang, H.

(2014) Bioorg.Med.Chem. 22: 6256-6269

  • DOI: 10.1016/j.bmc.2014.08.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An aminoquinazoline series targeting the essential bacterial enzyme GlmU (uridyltransferase) were previously reported (Biochem. J.2012, 446, 405). In this study, we further explored SAR through a combination of traditional medicinal chemistry and str ...

    An aminoquinazoline series targeting the essential bacterial enzyme GlmU (uridyltransferase) were previously reported (Biochem. J.2012, 446, 405). In this study, we further explored SAR through a combination of traditional medicinal chemistry and structure-based drug design, resulting in a novel scaffold (benzamide) with selectivity against protein kinases. Virtual screening identified fragments that could be fused into the core scaffold, exploiting additional binding interactions and thus improving potency. These efforts resulted in a hybrid compound with target potency increased by a 1000-fold, while maintaining selectivity against selected protein kinases and an improved level of solubility and protein binding. Despite these significant improvements no significant antibacterial activity was yet observed within this class.


    Organizational Affiliation

    Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States. Electronic address: Peter.Doig@astrazeneca.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional protein GlmU
A
456Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: glmU
Find proteins for P43889 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P43889
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1SF
Query on 1SF

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Download CCD File 
A
1-(3-nitrophenyl)dihydropyrimidine-2,4(1H,3H)-dione
C10 H9 N3 O4
GMUGBPYYXAGNCT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 108.751α = 90.00
b = 108.751β = 90.00
c = 327.488γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-17
    Type: Database references