2X9V | pdb_00002x9v

High resolution structure of TbPTR1 with trimetrexate

• PDB DOI: https://doi.org/10.2210/pdb2X9V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma brucei brucei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-24 Released: 2010-06-23 
• Deposition Author(s): Dawson, A., Tulloch, L.B., Barrack, K.L., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.148 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.121 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

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

• PubMed: 21123874 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 127.49 kDa 
• Atom Count: 9,148 
• Modelled Residue Count: 1,000 
• Deposited Residue Count: 1,152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTERIDINE REDUCTASE	A, B, C, D	288	Trypanosoma brucei brucei	Mutation(s): 0  EC: 1.5.1.33
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei) Explore O76290  Go to UniProtKB:  O76290

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], H [auth B], L [auth C], P [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
TMQ	F [auth A], I [auth B], M [auth C], Q [auth D]	TRIMETREXATE C19 H24 N5 O3 NOYPYLRCIDNJJB-UHFFFAOYSA-O
ACT	G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.148 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.121 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.56	α = 90
b = 90.71	β = 115.69
c = 82.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-23 
Deposition Author(s): Dawson, A., Tulloch, L.B., Barrack, K.L., Hunter, W.N.

Revision History  

• Version 1.0: 2010-06-23
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Database references, Refinement description, Version format compliance
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other