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- PDB-4ori: Rat dihydroorotate dehydrogenase bound with DSM338 (N-[3,5-difluo... -

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Basic information

Entry
Database: PDB / ID: 4ori
TitleRat dihydroorotate dehydrogenase bound with DSM338 (N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine)
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / alpha/beta barrel / Oxidoreductase / FMN / mitochondrial membrane / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Pyrimidine biosynthesis / response to L-arginine / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / UDP biosynthetic process / response to caffeine / regulation of mitochondrial fission ...Pyrimidine biosynthesis / response to L-arginine / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / UDP biosynthetic process / response to caffeine / regulation of mitochondrial fission / response to starvation / ubiquinone binding / 'de novo' UMP biosynthetic process / quinone binding / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / response to organic cyclic compound / FMN binding / mitochondrial inner membrane / response to xenobiotic stimulus / positive regulation of apoptotic process / neuronal cell body
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2V6 / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDeng, X. / Phillips, M.A.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Fluorine Modulates Species Selectivity in the Triazolopyrimidine Class of Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors.
Authors: Deng, X. / Kokkonda, S. / El Mazouni, F. / White, J. / Burrows, J.N. / Kaminsky, W. / Charman, S.A. / Matthews, D. / Rathod, P.K. / Phillips, M.A.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4214
Polymers40,4111
Non-polymers1,0103
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.365, 43.845, 63.305
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dihydroorotate dehydrogenase (quinone), mitochondrial / DHOdehase / Dihydroorotate oxidase


Mass: 40410.965 Da / Num. of mol.: 1 / Fragment: UNP residues 32-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dhodh, DIHYDROOROTATE DEHYDROGENASE / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): bl21
References: UniProt: Q63707, dihydroorotate dehydrogenase (quinone)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-2V6 / N-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine


Mass: 397.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H7F8N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.64 M Ammonium sulfate, 0.1 M Sodium Acetate, pH 4.2, 1.2 M NaCl, and 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 60412 / Num. obs: 56541 / % possible obs: 93.6 % / Observed criterion σ(F): 2.55 / Observed criterion σ(I): 2.55 / Redundancy: 4.7 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.064 / Net I/σ(I): 15.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.8 % / Num. unique all: 2731 / Rsym value: 0.425 / % possible all: 92.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UUO

1uuo


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.216 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 2.55 / ESU R: 0.089 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 2836 5 %RANDOM
Rwork0.18033 ---
obs0.18311 53464 95.43 %-
all-58921 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.316 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-2.26 Å2
2---0.07 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 69 111 2887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192841
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1662.0163861
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5695357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.31123.471121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381527
X-RAY DIFFRACTIONr_chiral_restr0.1410.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212146
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr11.22232839
X-RAY DIFFRACTIONr_sphericity_free31.958547
X-RAY DIFFRACTIONr_sphericity_bonded16.39452866
LS refinement shellResolution: 1.5→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 141 -
Rwork0.33 2931 -
obs-2731 92.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9738.21260.723421.6437-7.507517.50430.1520.0125-0.511-0.0223-0.8119-1.46790.74591.54150.65990.20010.13440.14910.38790.08130.37133.6804-30.48311.7168
25.90163.137-0.33394.2369-0.28654.44040.07910.0304-0.1145-0.0451-0.19080.0781-0.17840.1660.11180.12150.02950.03170.1665-0.02170.0735-4.6285-23.5613.1011
33.715-0.4855-0.73181.6529-0.49943.14820.0246-0.1265-0.4695-0.0994-0.0810.14390.7215-0.43090.05630.2079-0.0934-0.01670.1599-0.01880.1695-20.7194-36.127919.5778
41.49840.04341.21711.0688-0.38943.1803-0.08410.19670.0967-0.1341-0.0876-0.0075-0.25550.02440.17170.10640.0278-0.02280.0923-0.01480.0771-14.3616-19.90758.4701
51.82250.46731.00121.4293-0.28562.9601-0.05550.18080.0922-0.2196-0.04370.0774-0.1315-0.16220.09910.08730.052-0.03510.1002-0.03260.0757-19.2036-21.19925.8495
61.3217-0.0590.71571.6368-0.41671.6032-0.1261-0.12120.33520.01120.01360.0152-0.3764-0.3630.11250.13620.0839-0.06380.2134-0.05130.1657-26.8224-11.776411.4581
76.35160.32182.09362.2732-0.8261.5361-0.2157-0.15990.0761-0.05460.19680.3253-0.2311-0.5620.01890.10740.1543-0.03680.4177-0.09290.162-33.2304-14.101715.3673
834.410114.06869.46739.54825.80387.2797-0.2821-0.1918-0.21710.03730.03160.2559-0.6542-0.3130.25040.48290.22240.11360.2737-0.11160.2943-27.5712-7.007629.0613
91.38730.0690.88451.4192-0.3232.9427-0.0632-0.2120.08660.1016-0.07660.0042-0.126-0.21030.13970.07660.0128-0.01540.1003-0.03810.0626-13.0172-21.536525.6148
1020.78215.33260.003610.163812.229321.14060.2409-1.2126-0.21120.7094-0.4582-0.14810.8889-0.73260.21720.3479-0.03890.06460.6714-0.05650.2118-20.2626-23.654440.0011
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 46
2X-RAY DIFFRACTION2A47 - 67
3X-RAY DIFFRACTION3A68 - 89
4X-RAY DIFFRACTION4A90 - 138
5X-RAY DIFFRACTION5A139 - 173
6X-RAY DIFFRACTION6A174 - 231
7X-RAY DIFFRACTION7A232 - 259
8X-RAY DIFFRACTION8A260 - 275
9X-RAY DIFFRACTION9A276 - 390
10X-RAY DIFFRACTION10A391 - 396

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