4KNX

Hin GlmU Bound to WG176


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmc.2014.08.017
  • Primary Citation of Related Structures:  
    4KNR, 4KNX, 4KPX, 4KPZ, 4KQL

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional protein GlmU456Haemophilus influenzaeMutation(s): 0 
Gene Names: glmUHI_0642
EC: 2.7.7.23 (PDB Primary Data), 2.3.1.157 (PDB Primary Data)
UniProt
Find proteins for P43889 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P43889 
Go to UniProtKB:  P43889
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43889
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1S9
Query on 1S9

Download Ideal Coordinates CCD File 
B [auth A][(4-{[4-(benzoylamino)phenyl]amino}-6-methoxyquinazolin-7-yl)oxy]acetic acid
C24 H20 N4 O5
VAJKCEBFUQHYLC-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1S9 Binding MOAD:  4KNX IC50: 3200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.745α = 90
b = 108.745β = 90
c = 326.183γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations