3JQG

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine (AX6)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases.

Tulloch, L.B.Martini, V.P.Iulek, J.Huggan, J.K.Lee, J.H.Gibson, C.L.Smith, T.K.Suckling, C.J.Hunter, W.N.

(2010) J.Med.Chem. 53: 221-229

  • DOI: 10.1021/jm901059x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pteridine reductase (PTR1) is a target for drug development against Trypanosoma and Leishmania species, parasites that cause serious tropical diseases and for which therapies are inadequate. We adopted a structure-based approach to the design of nove ...

    Pteridine reductase (PTR1) is a target for drug development against Trypanosoma and Leishmania species, parasites that cause serious tropical diseases and for which therapies are inadequate. We adopted a structure-based approach to the design of novel PTR1 inhibitors based on three molecular scaffolds. A series of compounds, most newly synthesized, were identified as inhibitors with PTR1-species specific properties explained by structural differences between the T. brucei and L. major enzymes. The most potent inhibitors target T. brucei PTR1, and two compounds displayed antiparasite activity against the bloodstream form of the parasite. PTR1 contributes to antifolate drug resistance by providing a molecular bypass of dihydrofolate reductase (DHFR) inhibition. Therefore, combining PTR1 and DHFR inhibitors might improve therapeutic efficacy. We tested two new compounds with known DHFR inhibitors. A synergistic effect was observed for one particular combination highlighting the potential of such an approach for treatment of African sleeping sickness.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pteridine reductase 1
A, C
288Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 0 
EC: 1.5.1.33
Find proteins for Q581W1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q581W1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pteridine reductase 1
B, D
288Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 0 
EC: 1.5.1.33
Find proteins for Q581W1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q581W1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
AX6
Query on AX6

Download SDF File 
Download CCD File 
A, B, C, D
6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine
C12 H14 N4 O S
SMBANLHZRGNZKV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
A, C
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AX6Ki: 18000 nM BINDINGMOAD
AX6Ki: 18000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.531α = 90.00
b = 89.845β = 115.53
c = 82.437γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MAR345data collection
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description