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- PDB-9oni: Crystal structure of dihydrofolate reductase (DHFR) from the fila... -

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Basic information

Entry
Database: PDB / ID: 9oni
TitleCrystal structure of dihydrofolate reductase (DHFR) from the filarial nematode W. bancrofti in complex with NADPH and methotrexate (MTX)
Componentsdihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate reductases / NADPH / antifolate
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
METHOTREXATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / dihydrofolate reductase
Similarity search - Component
Biological speciesWuchereria bancrofti (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.44 Å
AuthorsFrey, K.M. / Kwarteng, S. / Goodey, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2025
Title: A virtual screening strategy to repurpose antifolate compounds as W. Bancrofti DHFR inhibitors.
Authors: Kwarteng, S. / Wilhelm, J. / Salama, M. / Salama, M. / Hollander, K. / Anderson, K.S. / Goodey, N.M. / Frey, K.M.
History
DepositionMay 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2803
Polymers22,0821
Non-polymers1,1982
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.586, 133.586, 76.198
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

21A-749-

HOH

31A-750-

HOH

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Components

#1: Protein dihydrofolate reductase


Mass: 22082.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wuchereria bancrofti (agent of lymphatic filariasis)
Production host: Escherichia coli (E. coli) / References: UniProt: A0AAF5PZP7, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 4.47 Å3/Da / Density % sol: 72.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM trisodium citrate, pH 5.4-6.4, 25% w/v PEG4000, 200 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→34.41 Å / Num. obs: 15368 / % possible obs: 86.92 % / Redundancy: 1.1 % / Biso Wilson estimate: 46.3 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rsym value: 0.064 / Net I/σ(I): 10.77
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 168 / CC1/2: 0.555 / Rpim(I) all: 0.405 / Rsym value: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.44→34.41 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 682 5.11 %Random selection
Rwork0.2255 ---
obs0.2286 13348 86.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 81 52 1545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051530
X-RAY DIFFRACTIONf_angle_d0.7822076
X-RAY DIFFRACTIONf_dihedral_angle_d17.921553
X-RAY DIFFRACTIONf_chiral_restr0.048221
X-RAY DIFFRACTIONf_plane_restr0.006260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.630.4094520.32061020X-RAY DIFFRACTION36
2.63-2.90.36781660.31612801X-RAY DIFFRACTION98
2.9-3.310.37571410.29072889X-RAY DIFFRACTION100
3.31-4.170.27541620.20222893X-RAY DIFFRACTION100
4.17-34.410.22941610.18693063X-RAY DIFFRACTION99

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