3EPX

Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-2-(hydroxymethyl)-1-(quinolin-8-ylmethyl)pyrrolidin-3,4-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors.

Versees, W.Goeminne, A.Berg, M.Vandemeulebroucke, A.Haemers, A.Augustyns, K.Steyaert, J.

(2009) Biochim.Biophys.Acta 1794: 953-960

  • DOI: 10.1016/j.bbapap.2009.02.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Diseases caused by parasitic protozoa remain a major health problem, mainly due to old toxic drugs and rising drug resistance. Nucleoside hydrolases are key enzymes of the purine salvage pathway of parasites from the Trypanosomatidae family and are c ...

    Diseases caused by parasitic protozoa remain a major health problem, mainly due to old toxic drugs and rising drug resistance. Nucleoside hydrolases are key enzymes of the purine salvage pathway of parasites from the Trypanosomatidae family and are considered as possible drug targets. N-Arylmethyl substituted iminoribitols have been developed as selective nanomolar affinity inhibitors against the purine-specific nucleoside hydrolase of Trypanosoma vivax. The current paper describes the crystal structures of the T. vivax nucleoside hydrolase in complex with two of these inhibitors, to 1.3 and 1.85 A resolution. These high resolution structures provide an accurate picture of the mode of binding of these inhibitors and their mechanism of transition-state mimicry, and are valuable tools to guide further inhibitor design. Comparison of the current structures with previously solved structures of the enzyme in complex with ground-state and transition-state-analogue inhibitors also allows for the elucidation of a detailed molecular mechanism of active-site loop opening/closing. These loop movements can be coupled to the complex kinetic mechanism of the T. vivax nucleoside hydrolase.


    Organizational Affiliation

    Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium. wversees@vub.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IAG-nucleoside hydrolase
A, B
338Trypanosoma vivaxMutation(s): 0 
Find proteins for Q9GPQ4 (Trypanosoma vivax)
Go to UniProtKB:  Q9GPQ4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
IMQ
Query on IMQ

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Download CCD File 
A, B
(2R,3R,4S)-2-(hydroxymethyl)-1-(quinolin-8-ylmethyl)pyrrolidine-3,4-diol
C15 H18 N2 O3
MZDAWIBFZPTLPG-VNHYZAJKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IMQKi: 10.8 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.422α = 90.00
b = 74.198β = 98.36
c = 73.553γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance