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- PDB-9huv: Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor F224 -

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Basic information

Entry
Database: PDB / ID: 9huv
TitleTrypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor F224
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / benzothiazole
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / ACETATE ION / Chem-NDP / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLandi, G. / Pozzi, C. / Mangani, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)603240European Union
CitationJournal: J.Med.Chem. / Year: 2025
Title: Design of 2-Aminobenzothiazole Derivatives Targeting Trypanosomatid PTR1 by a Multidisciplinary Fragment Hybridization Approach.
Authors: 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. / ...Authors: 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.
History
DepositionDec 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pteridine reductase
B: Pteridine reductase
C: Pteridine reductase
D: Pteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,62115
Polymers123,2684
Non-polymers4,35311
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22440 Å2
ΔGint-137 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.299, 89.614, 82.603
Angle α, β, γ (deg.)90.00, 115.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pteridine reductase


Mass: 30816.982 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290

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Non-polymers , 5 types, 676 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-A1IXS / 2-azanyl-~{N}-[2-(4-bromophenyl)ethyl]-1,3-benzothiazole-6-carboxamide


Mass: 376.271 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H14BrN3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 2-2.5 M sodium acetate, 0.1 M sodium citrate, pH5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9196 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 1.58→89.61 Å / Num. obs: 130968 / % possible obs: 98.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Net I/σ(I): 13.7
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 18830 / CC1/2: 0.902 / Rpim(I) all: 0.316 / Rrim(I) all: 0.631

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→74.66 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.617 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19846 6631 5.1 %RANDOM
Rwork0.17101 ---
obs0.17244 124306 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.018 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å2-0 Å2-0.94 Å2
2--4.49 Å2-0 Å2
3----1.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.58→74.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7342 0 257 665 8264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.64110807
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30251040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15922.601346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3521545
X-RAY DIFFRACTIONr_chiral_restr0.1060.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025928
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5052.6564043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4133.9545047
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1852.9753848
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.97939.13812791
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 516 -
Rwork0.341 9012 -
obs--96.73 %

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