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

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Basic information

Entry
Database: PDB / ID: 9mlt
TitleCrystal structure of dihydrofolate reductase (DHFR) from the filarial nematode W. bancrofti in complex with NADPH and [2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-cyanophenyl]acetic acid (TSD25 or OFD)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate reductase / antifolates
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-OFD / dihydrofolate reductase
Similarity search - Component
Biological speciesWuchereria bancrofti (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsFrey, K.M. / Goodey, N.M. / Kwarteng, S. / Wilhelm, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionDec 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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)23,5683
Polymers22,3821
Non-polymers1,1862
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-4 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.013, 134.013, 75.560
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-466-

HOH

21A-467-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 22381.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wuchereria bancrofti (agent of lymphatic filariasis)
Gene: WUBG_00817 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: J9F199, 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-OFD / [2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-cyanophenyl]acetic acid


Mass: 442.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H18N6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 4.38 Å3/Da / Density % sol: 71.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM tri-sodium citrate, 25% w/v PEG4000, 200 mM ammonium sulfate, pH 6.0, 6.3, 6.5
PH range: 6.0-6.5

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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: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.105→34.44 Å / Num. obs: 23710 / % possible obs: 93.22 % / Redundancy: 1.1 % / CC1/2: 1 / Net I/σ(I): 13.53
Reflection shellResolution: 2.105→2.2 Å / Mean I/σ(I) obs: 0.92 / Num. unique obs: 2499 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.12.1-5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.105→34.44 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 1150 5.21 %
Rwork0.2058 --
obs0.2071 22093 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.105→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 81 70 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.898
X-RAY DIFFRACTIONf_dihedral_angle_d19.92620
X-RAY DIFFRACTIONf_chiral_restr0.05224
X-RAY DIFFRACTIONf_plane_restr0.007263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.105-2.20.2921741226X-RAY DIFFRACTION45
2.2-2.320.31721490.27182743X-RAY DIFFRACTION100
2.32-2.460.3051460.26352763X-RAY DIFFRACTION100
2.46-2.650.30911570.24992766X-RAY DIFFRACTION100
2.65-2.920.27551520.23682787X-RAY DIFFRACTION100
2.92-3.340.27891480.23812810X-RAY DIFFRACTION100
3.34-4.210.19771610.17822840X-RAY DIFFRACTION100
4.21-100.1911630.17823008X-RAY DIFFRACTION100

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