9HUU | pdb_00009huu

Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor F223


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Design of 2-Aminobenzothiazole Derivatives Targeting Trypanosomatid PTR1 by a Multidisciplinary Fragment Hybridization Approach.

Panecka-Hofman, J.Linciano, P.Pohner, I.Dyguda-Kazimierowicz, E.Jedwabny, W.Landi, G.Santarem, N.Witt, G.Ellinger, B.Kuzikov, M.Luciani, R.Ferrari, S.Aiello, D.Mangani, S.Pozzi, C.Cordeiro-da-Silva, A.Gul, S.Costi, M.P.Wade, R.C.

(2025) J Med Chem 68: 20595-20618

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01799
  • Primary Citation Related Structures: 
    9HUP, 9HUT, 9HUU, 9HUV, 9HUW

  • PubMed Abstract: 

    Pteridine reductase 1 (PTR1) is a folate pathway enzyme essential for pathogenic trypanosomatids and a promising drug target for diseases such as sleeping sickness and leishmaniasis. Previous studies have shown that the 2-aminobenzothiazole moiety targets the PTR1 biopterin pocket, while 3,4-dichlorophenyl-containing compounds, such as I bind a different region of the Trypanosoma brucei PTR1 ( Tb PTR1) pocket. This study combines both moieties via various linkers, creating two compound series screened in silico against Tb PTR1 and Leishmania major PTR1 ( Lm PTR1). In the first series, five compounds were synthesized, and 1a and 1b emerged as potent Tb PTR1 inhibitors, with 1b also being active against Lm PTR1 and moderately effective against Leishmania infantum . Furthermore, structure-activity relationship analysis, supported by quantum calculations and crystallography, revealed meta-halogenation to be more favorable than para, although single halogenation reduced antiparasite effects. Our fragment hybridization approach led to less toxic, more effective compounds than I .


  • Organizational Affiliation
    • Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), D-69118 Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 127.53 kDa 
  • Atom Count: 8,266 
  • Modeled Residue Count: 1,000 
  • Deposited Residue Count: 1,156 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pteridine reductase
A, B, C, D
289Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PTR1
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
L [auth C],
N [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
A1IXQ
(Subject of Investigation/LOI)

Query on A1IXQ



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B],
O [auth D]
2-azanyl-~{N}-[2-(4-chlorophenyl)ethyl]-1,3-benzothiazole-6-carboxamide
C16 H14 Cl N3 O S
JTXCPDGCZHOONR-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
P [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
M [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.554α = 90
b = 90.585β = 115.62
c = 83.142γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union603240

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release