5VSJ | pdb_00005vsj

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 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 9HVClick on this verticalbar to view details

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 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 9HVClick on this verticalbar to view details

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