2X9G

High resolution structure of TbPTR1 in complex with Pemetrexed

PDB DOI: https://doi.org/10.2210/pdb2X9G/pdb

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

Deposited: 2010-03-18 Released: 2010-06-16
Deposition Author(s): Dawson, A., Barrack, K.L., Tulloch, L.B., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.147
R-Value Observed: 0.121

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 21123874 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 127.42 kDa
Atom Count: 9,354
Modelled Residue Count: 1,002
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O76290
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
LYA Query on LYA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain M [auth D] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C]	F [auth A], H [auth B], K [auth C], M [auth D]	2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID C₂₀ H₂₁ N₅ O₆ WBXPDJSOTKVWSJ-ZDUSSCGKSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.147
R-Value Observed: 0.121
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.72	α = 90
b = 90.57	β = 115.61
c = 82.58	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-06-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-06-16
Type: Initial release
Version 1.1: 2012-04-11
Changes: Database references, Refinement description, Version format compliance
Version 1.2: 2019-05-22
Changes: Data collection, Other, Refinement description
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other