3MCV

Structure of PTR1 from Trypanosoma brucei in ternary complex with 2,4-diamino-5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]-pyrimidine and NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 

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Ligand Structure Quality Assessment 


This is version 1.2 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 D Biol Crystallogr 66: 1334-1340

  • DOI: https://doi.org/10.1107/S0907444910040886
  • Primary Citation of Related Structures:  
    2X9G, 2X9N, 2X9V, 3MCV

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pteridine reductase
A, B, C, D
288Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PTR1
EC: 1.5.1.33
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei)
Explore O76290 
Go to UniProtKB:  O76290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76290
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
N [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
MCV
Query on MCV

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
O [auth D]
5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]pyrimidine-2,4-diamine
C16 H18 N4 O2 S
XJFDLPAAAIBWID-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
K [auth B],
P [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.502α = 90
b = 89.819β = 115.49
c = 82.26γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations