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

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Basic information

Entry
Database: PDB / ID: 9ooi
TitleCrystal structure of dihydrofolate reductase (DHFR) from the filarial nematode W. bancrofti in complex with NADPH and antifolate 2-({4-[(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)benzoic acid (OG7 or TSD001)
Componentsdihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate reductase / antifolate / NADPH
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-OG7 / dihydrofolate reductase
Similarity search - Component
Biological speciesWuchereria bancrofti (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsFrey, K.M. / Goodey, N.M. / Kwarteng, S.
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
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
B: dihydrofolate reductase
C: dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0759
Polymers66,6353
Non-polymers3,4406
Water362
1
A: dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3583
Polymers22,2121
Non-polymers1,1472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3583
Polymers22,2121
Non-polymers1,1472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3583
Polymers22,2121
Non-polymers1,1472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.168, 232.027, 75.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein dihydrofolate reductase


Mass: 22211.602 Da / Num. of mol.: 3
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.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-OG7 / 2-({4-[(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)benzoic acid


Mass: 403.391 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H17N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 72.16 %
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: Feb 14, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.91→29.64 Å / Num. obs: 25197 / % possible obs: 95.78 % / Redundancy: 1 % / Rmerge(I) obs: 0.1875 / Net I/σ(I): 10.5
Reflection shellResolution: 2.91→3.01 Å / Rmerge(I) obs: 0.279 / Num. unique obs: 2345 / CC1/2: 1 / % possible all: 81.74

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→29.64 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2919 1228 4.87 %
Rwork0.2572 --
obs0.2589 25197 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 0 2 4544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024656
X-RAY DIFFRACTIONf_angle_d0.6156318
X-RAY DIFFRACTIONf_dihedral_angle_d14.5561853
X-RAY DIFFRACTIONf_chiral_restr0.047668
X-RAY DIFFRACTIONf_plane_restr0.004787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.030.32791130.28152232X-RAY DIFFRACTION82
3.03-3.160.32391180.28582481X-RAY DIFFRACTION90
3.17-3.330.2721480.2772552X-RAY DIFFRACTION94
3.33-3.540.36151280.26532720X-RAY DIFFRACTION98
3.54-3.810.27151110.25672784X-RAY DIFFRACTION99
3.81-4.20.26241400.23462741X-RAY DIFFRACTION99
4.2-4.80.28441640.22882758X-RAY DIFFRACTION100
4.8-6.040.30861670.25332753X-RAY DIFFRACTION100
6.04-29.640.26481390.27132948X-RAY DIFFRACTION100

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