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- PDB-9hut: Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor F222 -

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Basic information

Entry
Database: PDB / ID: 9hut
TitleTrypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor F222
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
: / Chem-NDP / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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)127,70114
Polymers123,2684
Non-polymers4,43310
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20230 Å2
ΔGint-122 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.337, 90.775, 83.210
Angle α, β, γ (deg.)90.00, 115.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#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-A1IXP / 2-azanyl-~{N}-[2-(3-chlorophenyl)ethyl]-1,3-benzothiazole-6-carboxamide


Mass: 331.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14ClN3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.86 %
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: 0.97622 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: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.84→90.77 Å / Num. obs: 84980 / % possible obs: 98.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 12
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 12503 / CC1/2: 0.812 / Rpim(I) all: 0.34 / Rrim(I) all: 0.673

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→75.12 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.5 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25266 4218 5 %RANDOM
Rwork0.19761 ---
obs0.20034 80735 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.821 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.84→75.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7352 0 288 485 8125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.64810693
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5751007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1622.522337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.288151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2751544
X-RAY DIFFRACTIONr_chiral_restr0.1050.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025860
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_it3.2053.5244016
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3755.2565003
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6953.8333812
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.12150.79412528
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: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 332 -
Rwork0.328 5997 -
obs--99.22 %

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