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- PDB-9n6o: Crystal structure of dihydroorotate dehydrogenase from Leishmania... -

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Basic information

Entry
Database: PDB / ID: 9n6o
TitleCrystal structure of dihydroorotate dehydrogenase from Leishmania braziliensis in complex with 5-(4-hydroxy-3-methoxybenzyl)pyrimidine-2,4,6(1H,3H,5H)-trione
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / LbDHODH / covalent / inhibitor
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania braziliensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFroes, T.Q. / Vaidergorn, M.M. / Leite, P.I.P.L. / Godoi, B.F. / dos Santos, T. / Emery, F.S. / Nonato, M.C.
Funding support Brazil, United States, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2019/ 25532-1 Brazil
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01AI160379-01 United States
CitationJournal: J.Med.Chem. / Year: 2025
Title: Barbituric Acid Derivatives as Covalent Inhibitors of Leishmania braziliensis Dihydroorotate Dehydrogenase.
Authors: Froes, T.Q. / Alegbejo Price, T.O. / Fleck Godoi, B. / Vaidergorn, M.M. / Dos Santos, T. / Leite, P.I.P. / Silva, D.G. / Dias da Purificacao, A. / Loch, L. / Schenkman, S. / Kratz, J.M. / da ...Authors: Froes, T.Q. / Alegbejo Price, T.O. / Fleck Godoi, B. / Vaidergorn, M.M. / Dos Santos, T. / Leite, P.I.P. / Silva, D.G. / Dias da Purificacao, A. / Loch, L. / Schenkman, S. / Kratz, J.M. / da Silva Emery, F. / Nonato, M.C.
History
DepositionFeb 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 8, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase
B: Dihydroorotate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,71711
Polymers74,8042
Non-polymers1,9149
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.040, 104.290, 107.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydroorotate dehydrogenase


Mass: 37401.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis (eukaryote) / Gene: DHODH, LBRM_16_0550 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E9AI53, EC: 1.3.3.1

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Non-polymers , 5 types, 139 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-A1BZM / 5-[(4-hydroxy-3-methoxyphenyl)methyl]-1,3-diazinane-2,4,6-trione


Mass: 264.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.2M ammonium sulfate, 0.25M lithium sulfate, 0.1M sodium citrate pH5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 1.9→47.74 Å / Num. obs: 105966 / % possible obs: 99.95 % / Redundancy: 7 % / Biso Wilson estimate: 35.25 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→1.92 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3555 / CC1/2: 0.436

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Processing

Software
NameVersionClassification
Coot0.9.8.93model building
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.68 Å / SU ML: 0.2572 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 23.7704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 5291 5 %
Rwork0.182 100627 -
obs0.1837 105918 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 89 130 4818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754818
X-RAY DIFFRACTIONf_angle_d1.13746547
X-RAY DIFFRACTIONf_chiral_restr0.0737720
X-RAY DIFFRACTIONf_plane_restr0.0076833
X-RAY DIFFRACTIONf_dihedral_angle_d12.5656694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.37451790.39493346X-RAY DIFFRACTION99.16
1.92-1.940.38751750.33513369X-RAY DIFFRACTION100
1.94-1.970.35231790.32933354X-RAY DIFFRACTION100
1.97-1.990.34741760.31353346X-RAY DIFFRACTION100
1.99-2.020.3391750.30073343X-RAY DIFFRACTION100
2.02-2.050.28191770.29743377X-RAY DIFFRACTION100
2.05-2.080.29321800.27423372X-RAY DIFFRACTION100
2.08-2.110.29311770.25523327X-RAY DIFFRACTION99.94
2.11-2.140.3221780.2473361X-RAY DIFFRACTION100
2.14-2.170.22411750.22873351X-RAY DIFFRACTION100
2.17-2.210.23811750.22353371X-RAY DIFFRACTION100
2.21-2.250.25781750.20663338X-RAY DIFFRACTION100
2.25-2.30.22061740.20083367X-RAY DIFFRACTION100
2.3-2.340.21241770.20023359X-RAY DIFFRACTION100
2.34-2.390.26291730.19253321X-RAY DIFFRACTION100
2.39-2.450.21311740.19953360X-RAY DIFFRACTION100
2.45-2.510.2541780.20093360X-RAY DIFFRACTION99.97
2.51-2.580.22781800.1933390X-RAY DIFFRACTION100
2.58-2.650.22631760.18833329X-RAY DIFFRACTION100
2.65-2.740.24761790.1843345X-RAY DIFFRACTION100
2.74-2.840.22091780.17813358X-RAY DIFFRACTION100
2.84-2.950.24631780.17923380X-RAY DIFFRACTION100
2.95-3.090.19921740.18523345X-RAY DIFFRACTION100
3.09-3.250.21891700.1733363X-RAY DIFFRACTION100
3.25-3.450.18441780.16783359X-RAY DIFFRACTION99.94
3.45-3.720.21671690.14983322X-RAY DIFFRACTION99.94
3.72-4.090.1821760.14383353X-RAY DIFFRACTION100
4.09-4.680.14441730.13383372X-RAY DIFFRACTION100
4.69-5.90.17621790.15723348X-RAY DIFFRACTION100
5.9-47.680.21461840.16773341X-RAY DIFFRACTION99.69

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