4AA7 | pdb_00004aa7

E.coli GlmU in complex with an antibacterial inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4AA7/pdb

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


• Deposited: 2011-11-30 Released: 2012-08-15 
• Deposition Author(s): Otterbein, L., Breed, J., Ogg, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.179 (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.

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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 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.51 kDa 
• Atom Count: 3,726 
• Modeled Residue Count: 443 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BIFUNCTIONAL PROTEIN GLMU	A, B	231	Escherichia coli K-12	Mutation(s): 0  EC: 2.3.1.157 (PDB Primary Data), 2.7.7.23 (PDB Primary Data)
UniProt
Find proteins for P0ACC7 (Escherichia coli (strain K12)) Explore P0ACC7  Go to UniProtKB:  P0ACC7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R82	C [auth A], E [auth B]	N-(2,4-dimethoxy-5-{[(2R)-2-methyl-2,3-dihydro-1H-indol-1-yl]sulfonyl}phenyl)acetamide C19 H22 N2 O5 S WCESRWVTCVMYMU-GFCCVEGCSA-N
SO4	D [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
R82	BindingDB:  4AA7	IC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.713	α = 90
b = 80.713	β = 90
c = 140.061	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Otterbein, L., Breed, J., Ogg, D.J.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Data collection
• Version 1.2: 2017-12-27
  Changes: Database references
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description