4AAW | pdb_00004aaw

S.pneumoniae GlmU in complex with an antibacterial inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4AAW/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2011-12-05 Released: 2012-02-15 
• Deposition Author(s): Otterbein, L., Breed, J., Ogg, D.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.237 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Inhibitors of Acetyltransferase Domain of N-Acetylglucosamine-1-Phosphate-Uridyltransferase/ Glucosamine-1-Phosphate-Acetyltransferase (Glmu). Part 1: Hit to Lead Evaluation of a Novel Arylsulfonamide Series.

Green, O.M., McKenzie, A.R., Shapiro, A.B., Otterbein, L., Ni, H., Patten, A., Stokes, S., Albert, R., Kawatkar, S., Breed, J.

(2012) Bioorg Med Chem Lett 22: 1510

• PubMed: 22297115 
• DOI: https://doi.org/10.1016/j.bmcl.2012.01.016
• Primary Citation Related Structures: 
  4AA7, 4AAW, 4AC3


• PubMed Abstract: 
  

  A novel arylsulfonamide-containing series of compounds represented by 1, discovered by highthroughput screening, inhibit the acetyltransferase domain of N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU). X-ray structure determination confirmed that inhibitor binds at the site occupied by acetyl-CoA, indicating that series is competitive with this substrate. This letter documents our early hit-to-lead evaluation of the chemical series and some of the findings that led to improvement in in-vitro potency against Gram-negative and Gram-positive bacterial isozymes, exemplified by compound 40.

---

Organizational Affiliation: 
• Infection Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, MA 02451, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.21 kDa 
• Atom Count: 3,790 
• Modeled Residue Count: 455 
• Deposited Residue Count: 459 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BIFUNCTIONAL PROTEIN GLMU	A	459	Streptococcus pneumoniae	Mutation(s): 0  EC: 2.3.1.157 (PDB Primary Data), 2.7.7.23 (PDB Primary Data)
UniProt
Find proteins for Q8DQ18 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DQ18  Go to UniProtKB:  Q8DQ18

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R84	B [auth A]	4-{[1-(2-{[({5-[(3-carboxypropanoyl)amino]-2,4-dimethoxyphenyl}sulfonyl)amino]methyl}phenyl)piperidin-4-yl]methoxy}-4-oxobutanoic acid C29 H37 N3 O11 S PRDHHOYRFMTLDT-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
R84	BindingDB:  4AAW	IC50: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.237 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.779	α = 90
b = 116.779	β = 90
c = 116.683	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Otterbein, L., Breed, J., Ogg, D.J.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-08-15
  Changes: Database references
• Version 1.2: 2017-12-27
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description