5VSJ

Sco GlgEI-V279S in complex with a pyrolidene-based ethyl-phosphonate compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Zwitterionic pyrrolidene-phosphonates: inhibitors of the glycoside hydrolase-like phosphorylase Streptomyces coelicolor GlgEI-V279S.

Veleti, S.K.Petit, C.Ronning, D.R.Sucheck, S.J.

(2017) Org Biomol Chem 15: 3884-3891

  • DOI: https://doi.org/10.1039/c7ob00388a
  • Primary Citation of Related Structures:  
    5VSJ, 5VT4

  • PubMed Abstract: 

    We synthesized and evaluated new zwitterionic inhibitors against glycoside hydrolase-like phosphorylase Streptomyces coelicolor (Sco) GlgEI-V279S which plays a role in α-glucan biosynthesis. Sco GlgEI-V279S serves as a model enzyme for validated anti-tuberculosis (TB) target Mycobacterium tuberculosis (Mtb) GlgE. Pyrrolidine inhibitors 5 and 6 were designed based on transition state considerations and incorporate a phosphonate on the pyrrolidine moiety to expand the interaction network between the inhibitor and the enzyme active site. Compounds 5 and 6 inhibited Sco GlgEI-V279S with K i = 45 ± 4 μM and 95 ± 16 μM, respectively, and crystal structures of Sco GlgE-V279S-5 and Sco GlgE-V279S-6 were obtained at a 3.2 Å and 2.5 Å resolution, respectively.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry and School of Green Chemistry and Engineering, The University of Toledo, 2801 W. Bancroft Street, Toledo, Ohio 43606, USA. steve.sucheck@utoledo.edu donald.ronning@utoledo.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
A, B
663Streptomyces coelicolor A3(2)Mutation(s): 1 
Gene Names: glgE1pep1pep1Apep1ISCO5443SC6A11.19c
EC: 2.4.99.16
UniProt
Find proteins for Q9L1K2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9L1K2 
Go to UniProtKB:  Q9L1K2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L1K2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9HV
Query on 9HV

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
{2-[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]ethyl}phosphonic acid
C14 H28 N O12 P
QLKUMDMMFYIFJS-IDWYSJKESA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.855α = 90
b = 113.855β = 90
c = 317.306γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI105084

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Advisory, Author supporting evidence
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description