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- PDB-9qdk: Trypanosoma brucei PTR1 in complex with fragment L330 and compound F46 -

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Basic information

Entry
Database: PDB / ID: 9qdk
TitleTrypanosoma brucei PTR1 in complex with fragment L330 and compound F46
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / fragment based drug design / NADPH
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 / 1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine / Chem-NDP / 2-amino-3H,4H,7H-pyrrolo[2,3-d]pyrimidin-4-one / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLandi, G. / Mangani, S. / Pozzi, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)603240European Union
CitationJournal: To Be Published
Title: Identification and optimization of Trypanosoma Brucei Pteridine-Reductase 1 Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design
Authors: Linciano, P. / Landi, G. / Mangani, S. / Pozzi, C. / Costi, M.P.
History
DepositionMar 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: 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)127,64019
Polymers122,6794
Non-polymers4,96115
Water11,295627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.505, 89.298, 82.629
Angle α, β, γ (deg.)90.00, 115.65, 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: 30669.791 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 , 6 types, 642 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-QY8 / 2-amino-3H,4H,7H-pyrrolo[2,3-d]pyrimidin-4-one / 2-azanyl-3,7-dihydropyrrolo[2,3-d]pyrimidin-4-one


Mass: 150.138 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-AX8 / 1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine


Mass: 292.163 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11Cl2N3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.74 %
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 18, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44.65 Å / Num. obs: 76418 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.061 / Rrim(I) all: 0.108 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2 / Num. unique obs: 11160 / CC1/2: 0.827 / Rpim(I) all: 0.389 / Rrim(I) all: 0.687

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.358 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21673 3895 5.1 %RANDOM
Rwork0.17061 ---
obs0.17299 72463 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.815 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.9→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7269 0 326 627 8222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127855
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.65710754
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29951012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89722.493341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.576151201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1641545
X-RAY DIFFRACTIONr_chiral_restr0.0970.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025897
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_it1.6462.0753983
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4923.0944968
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0072.3083872
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.80130.2712838
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 287 -
Rwork0.316 5338 -
obs--99.65 %

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