2X9V

High resolution structure of TbPTR1 with trimetrexate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High-Resolution Structures of Trypanosoma Brucei Pteridine Reductase Ligand Complexes Inform on the Placement of New Molecular Entities in the Active Site of a Potential Drug Target

Dawson, A.Tulloch, L.B.Barrack, K.L.Hunter, W.N.

(2010) Acta Crystallogr.,Sect.D 66: 1334

  • DOI: 10.1107/S0907444910040886
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pteridine reductase (PTR1) is a potential target for drug development against parasitic Trypanosoma and Leishmania species. These protozoa cause serious diseases for which current therapies are inadequate. High-resolution structures have been determi ...

    Pteridine reductase (PTR1) is a potential target for drug development against parasitic Trypanosoma and Leishmania species. These protozoa cause serious diseases for which current therapies are inadequate. High-resolution structures have been determined, using data between 1.6 and 1.1 Å resolution, of T. brucei PTR1 in complex with pemetrexed, trimetrexate, cyromazine and a 2,4-diaminopyrimidine derivative. The structures provide insight into the interactions formed by new molecular entities in the enzyme active site with ligands that represent lead compounds for structure-based inhibitor development and to support early-stage drug discovery.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD15EH, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PTERIDINE REDUCTASE
A, B, C, D
288Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PTR1
Find proteins for O76290 (Trypanosoma brucei brucei)
Go to UniProtKB:  O76290
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
TMQ
Query on TMQ

Download SDF File 
Download CCD File 
A, B, C, D
TRIMETREXATE
C19 H24 N5 O3
NOYPYLRCIDNJJB-UHFFFAOYSA-O
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TMQKi: ~70 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.121 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.560α = 90.00
b = 90.710β = 115.69
c = 82.460γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2012-04-11
    Type: Database references, Refinement description, Version format compliance