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- PDB-6rx5: Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 1 (NMT... -

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Basic information

Entry
Database: PDB / ID: 6rx5
TitleTrypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 1 (NMT-C0003)
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / pteridine based inhibitors
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-FE1 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsLandi, G. / Pozzi, C. / Mangani, S.
Funding support1items
OrganizationGrant numberCountry
European Union603240
CitationJournal: J.Med.Chem. / Year: 2022
Title: Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1.
Authors: Pohner, I. / Quotadamo, A. / Panecka-Hofman, J. / Luciani, R. / Santucci, M. / Linciano, P. / Landi, G. / Di Pisa, F. / Dello Iacono, L. / Pozzi, C. / Mangani, S. / Gul, S. / Witt, G. / ...Authors: Pohner, I. / Quotadamo, A. / Panecka-Hofman, J. / Luciani, R. / Santucci, M. / Linciano, P. / Landi, G. / Di Pisa, F. / Dello Iacono, L. / Pozzi, C. / Mangani, S. / Gul, S. / Witt, G. / Ellinger, B. / Kuzikov, M. / Santarem, N. / Cordeiro-da-Silva, A. / Costi, M.P. / Venturelli, A. / Wade, R.C.
History
DepositionJun 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)127,15513
Polymers122,6794
Non-polymers4,4769
Water16,286904
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint-139 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.860, 90.700, 82.950
Angle α, β, γ (deg.)90.00, 115.73, 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 , 5 types, 913 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FE1 / METHYL 1-(4-{[(2,4-DIAMINOPTERIDIN-6-YL)METHYL](METHYL)AMINO}BENZOYL)PIPERIDINE-4-CARBOXYLATE / 903R


Mass: 450.494 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H26N8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 / 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: I04-1 / Wavelength: 0.91731 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91731 Å / Relative weight: 1
ReflectionResolution: 1.42→57.67 Å / Num. obs: 187289 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 11.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.031 / Rrim(I) all: 0.062 / Net I/σ(I): 11
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 27201 / CC1/2: 0.926 / Rpim(I) all: 0.17 / Rrim(I) all: 0.337 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDC

5jdc


Resolution: 1.42→57.67 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.296 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.056
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 9189 4.9 %RANDOM
Rwork0.13764 ---
obs0.13948 178068 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.928 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.02 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.148 Å
Refinement stepCycle: 1 / Resolution: 1.42→57.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7259 0 301 904 8464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197915
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6982.00610870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79751051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50524.276290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.057151222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0091545
X-RAY DIFFRACTIONr_chiral_restr0.1060.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215906
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_it1.4284032
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7775046
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9313883
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.25612875
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.85637165
X-RAY DIFFRACTIONr_sphericity_free25.8945393
X-RAY DIFFRACTIONr_sphericity_bonded11.73857418
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 669 -
Rwork0.217 13098 -
obs--99.33 %

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