4KPZ | pdb_00004kpz

Hin GlmU bound to a small molecule fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.226 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4KPZ

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 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.

Macromolecule Content 

  • Total Structure Weight: 50.59 kDa 
  • Atom Count: 4,012 
  • Modeled Residue Count: 450 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1SF

Query on 1SF



Download:Ideal Coordinates CCD File
B [auth A]1-(3-nitrophenyl)dihydropyrimidine-2,4(1H,3H)-dione
C10 H9 N3 O4
GMUGBPYYXAGNCT-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.751α = 90
b = 108.751β = 90
c = 327.488γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata 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