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

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Basic information

Entry
Database: PDB / ID: 9mlm
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-methoxyphenyl]acetic acid (TSD10 or OED)
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
Chem-NDP / Chem-OED / dihydrofolate reductase
Similarity search - Component
Biological speciesWuchereria bancrofti (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsFrey, K.M. / Goodey, N.M. / Kwarteng, S. / Wilhelm, J.
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
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)24,3204
Polymers22,3821
Non-polymers1,9383
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-2 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.496, 133.496, 75.317
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-761-

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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H30N7O17P3
#3: Chemical ChemComp-OED / [2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-methoxyphenyl]acetic acid


Mass: 447.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N5O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.42 Å3/Da / Density % sol: 72.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 5% 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: Aug 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→33.37 Å / Num. obs: 37923 / % possible obs: 88.01 % / Redundancy: 1.1 % / Biso Wilson estimate: 27.99 Å2 / CC1/2: 1 / Net I/σ(I): 10.55
Reflection shellResolution: 1.79→1.84 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6434 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→33.37 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1606 4.81 %
Rwork0.2175 --
obs0.2191 33365 88.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 81 62 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.897
X-RAY DIFFRACTIONf_dihedral_angle_d19.076562
X-RAY DIFFRACTIONf_chiral_restr0.055222
X-RAY DIFFRACTIONf_plane_restr0.008264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.3471900.31923173X-RAY DIFFRACTION99
1.84-1.90.29971222397X-RAY DIFFRACTION82
1.93-1.990.31241230.25782518X-RAY DIFFRACTION99
1.99-2.050.2561280.24352377X-RAY DIFFRACTION100
2.1-2.190.24881320.22682549X-RAY DIFFRACTION100
2.19-2.320.26451230.22312410X-RAY DIFFRACTION74
2.32-2.50.24491640.22543261X-RAY DIFFRACTION100
2.5-2.750.25141500.23083301X-RAY DIFFRACTION100
2.75-3.150.25141680.23083294X-RAY DIFFRACTION100
3.15-3.970.26341420.21022938X-RAY DIFFRACTION88
3.97-100.21491640.18563541X-RAY DIFFRACTION100

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