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- PDB-9n6q: Crystal structure of dihydroorotate dehydrogenase from Leishmania... -

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Basic information

Entry
Database: PDB / ID: 9n6q
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: 1.85 Å
AuthorsFroes, T.Q. / Vaidergorn, M.M. / Leite, P.I.P. / 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)76,60112
Polymers74,8042
Non-polymers1,79710
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-110 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.720, 105.470, 106.120
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, 276 molecules

#2: Chemical ChemComp-A1BWI / 5-ethyl-1,3-diazinane-2,4,6-trione


Mass: 156.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.6M ammonium sulfate, 0.25M lithium sulfate, 0.1M sodium citrate

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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: Jun 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 1.85→47.6 Å / Num. obs: 59862 / % possible obs: 99.98 % / Redundancy: 7.1 % / Biso Wilson estimate: 40.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shellResolution: 1.85→1.87 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3836 / CC1/2: 0.461

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286-000refinement
Coot0.9.8.93model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.09 Å / SU ML: 0.2943 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2099 5705 4.99 %
Rwork0.1738 108512 -
obs0.1756 59848 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.83 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 115 266 4920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00984776
X-RAY DIFFRACTIONf_angle_d0.94836481
X-RAY DIFFRACTIONf_chiral_restr0.0717705
X-RAY DIFFRACTIONf_plane_restr0.009826
X-RAY DIFFRACTIONf_dihedral_angle_d10.6861677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.45771940.4043641X-RAY DIFFRACTION99.92
1.87-1.890.39331860.3623603X-RAY DIFFRACTION99.97
1.89-1.920.351900.32313627X-RAY DIFFRACTION100
1.92-1.940.31341920.31193610X-RAY DIFFRACTION100
1.94-1.970.34851890.29363591X-RAY DIFFRACTION99.95
1.97-1.990.28771950.28053644X-RAY DIFFRACTION100
1.99-2.020.24781850.28413614X-RAY DIFFRACTION100
2.02-2.050.33241920.28013645X-RAY DIFFRACTION100
2.05-2.080.35031890.26653579X-RAY DIFFRACTION99.92
2.08-2.120.30981930.24973628X-RAY DIFFRACTION100
2.12-2.150.2381910.23653619X-RAY DIFFRACTION100
2.15-2.190.27381910.22153611X-RAY DIFFRACTION100
2.19-2.240.26671900.2253588X-RAY DIFFRACTION100
2.24-2.280.26391850.20623660X-RAY DIFFRACTION100
2.28-2.330.24681930.20683579X-RAY DIFFRACTION100
2.33-2.390.2341890.19973631X-RAY DIFFRACTION100
2.39-2.440.24661910.19643647X-RAY DIFFRACTION100
2.44-2.510.27151920.19763605X-RAY DIFFRACTION100
2.51-2.580.2081920.19993613X-RAY DIFFRACTION100
2.58-2.670.2371920.18853623X-RAY DIFFRACTION100
2.67-2.760.20671930.17963569X-RAY DIFFRACTION100
2.76-2.870.24061930.17593641X-RAY DIFFRACTION100
2.87-30.21031900.17293629X-RAY DIFFRACTION100
3-3.160.21851910.17633601X-RAY DIFFRACTION100
3.16-3.360.19731890.16853603X-RAY DIFFRACTION100
3.36-3.620.22011890.14733645X-RAY DIFFRACTION100
3.62-3.980.18071790.14023602X-RAY DIFFRACTION100
3.98-4.560.16111900.11683632X-RAY DIFFRACTION100
4.56-5.740.15981880.13333611X-RAY DIFFRACTION100
5.74-40.090.16941920.17223621X-RAY DIFFRACTION99.69

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