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- PDB-9n67: Crystal structure of dihydroorotate dehydrogenase from Leishmania... -

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Basic information

Entry
Database: PDB / ID: 9n67
TitleCrystal structure of dihydroorotate dehydrogenase from Leishmania braziliensis in complex with orotate
ComponentsDihydroorotate dehydrogenase
KeywordsOXIDOREDUCTASE / LbDHODH / covalent / inhibitor / orotate
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 / OROTIC ACID / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesLeishmania braziliensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFroes, T.Q. / Vaidergorn, M.M. / 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

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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)76,68913
Polymers74,8042
Non-polymers1,88511
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-90 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.980, 105.456, 106.095
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, 575 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: Ammonium sulfate, lithium sulfate, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.8→47.72 Å / Num. obs: 65143 / % possible obs: 99.98 % / Redundancy: 11.6 % / Biso Wilson estimate: 24.06 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9371 / CC1/2: 0.696 / % possible all: 100

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Processing

Software
NameVersionClassification
Coot1.20.1_4487model building
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.72 Å / SU ML: 0.185 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8917
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2025 2006 3.08 %
Rwork0.1648 63123 -
obs0.166 65129 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 122 564 5302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01434905
X-RAY DIFFRACTIONf_angle_d1.23996662
X-RAY DIFFRACTIONf_chiral_restr0.0814721
X-RAY DIFFRACTIONf_plane_restr0.0108856
X-RAY DIFFRACTIONf_dihedral_angle_d11.6918703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.26561440.22584423X-RAY DIFFRACTION100
1.85-1.890.29411390.2284470X-RAY DIFFRACTION100
1.89-1.950.31321420.21974444X-RAY DIFFRACTION100
1.95-2.010.28671430.21024450X-RAY DIFFRACTION100
2.01-2.090.21971400.19054473X-RAY DIFFRACTION99.98
2.09-2.170.23081430.18124455X-RAY DIFFRACTION100
2.17-2.270.22581440.18284483X-RAY DIFFRACTION99.98
2.27-2.390.20111420.18394495X-RAY DIFFRACTION99.98
2.39-2.540.23351370.17544476X-RAY DIFFRACTION100
2.54-2.730.24551420.17554513X-RAY DIFFRACTION99.94
2.73-3.010.2151450.17164516X-RAY DIFFRACTION99.91
3.01-3.440.18421430.16014557X-RAY DIFFRACTION99.98
3.44-4.340.15531450.12984585X-RAY DIFFRACTION100
4.34-47.720.15881570.13884783X-RAY DIFFRACTION99.9

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