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- PDB-6j3c: Crystal structure of human DHODH in complex with inhibitor 1291 -

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Basic information

Entry
Database: PDB / ID: 6j3c
TitleCrystal structure of human DHODH in complex with inhibitor 1291
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DHODH / Inhibitor / Complex / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / cytosol
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 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-B5X / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsYu, Y. / Chen, Q.
CitationJournal: Febs Open Bio / Year: 2019
Title: A novel series of human dihydroorotate dehydrogenase inhibitors discovered by in vitro screening: inhibition activity and crystallographic binding mode.
Authors: Zeng, T. / Zuo, Z. / Luo, Y. / Zhao, Y. / Yu, Y. / Chen, Q.
History
DepositionJan 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,3629
Polymers39,7251
Non-polymers1,6378
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-54 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.596, 90.596, 122.803
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 39725.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli (E. coli)
References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 6 types, 290 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Chemical ChemComp-B5X / (6R)-1-[4-[3-(dimethylamino)phenyl]-3,5-bis(fluoranyl)phenyl]-6-propan-2-yl-6,7-dihydro-5H-benzotriazol-4-one


Mass: 410.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24F2N4O
#6: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H31NO / Comment: LDAO, detergent*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: hepes pH4.6, 2M AMMONIUM SULPHATE, 30% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 50299 / % possible obs: 100 % / Redundancy: 9.9 % / Rpim(I) all: 0.053 / Net I/σ(I): 13
Reflection shellResolution: 1.89→1.95 Å / Num. unique obs: 3312 / Rpim(I) all: 0.318

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.851→40.934 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.14
RfactorNum. reflection% reflection
Rfree0.1951 2496 5 %
Rwork0.1689 --
obs0.1703 49917 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.851→40.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 108 282 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072930
X-RAY DIFFRACTIONf_angle_d1.0183971
X-RAY DIFFRACTIONf_dihedral_angle_d14.9191095
X-RAY DIFFRACTIONf_chiral_restr0.041437
X-RAY DIFFRACTIONf_plane_restr0.005514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8508-1.88640.26041120.24632429X-RAY DIFFRACTION91
1.8864-1.92490.24791320.22092561X-RAY DIFFRACTION99
1.9249-1.96680.23491460.20542617X-RAY DIFFRACTION100
1.9668-2.01250.22471060.18532662X-RAY DIFFRACTION100
2.0125-2.06290.21491340.18932618X-RAY DIFFRACTION100
2.0629-2.11860.21861460.18342615X-RAY DIFFRACTION100
2.1186-2.1810.18291220.17122607X-RAY DIFFRACTION100
2.181-2.25140.20351440.16572620X-RAY DIFFRACTION100
2.2514-2.33180.17831530.15752614X-RAY DIFFRACTION100
2.3318-2.42520.18451470.15662648X-RAY DIFFRACTION100
2.4252-2.53550.20071340.15682623X-RAY DIFFRACTION100
2.5355-2.66920.17511330.15842669X-RAY DIFFRACTION100
2.6692-2.83640.1591420.16062645X-RAY DIFFRACTION100
2.8364-3.05530.20381360.15792646X-RAY DIFFRACTION100
3.0553-3.36270.17641500.15672669X-RAY DIFFRACTION100
3.3627-3.84890.18521560.14462671X-RAY DIFFRACTION100
3.8489-4.8480.16441420.15212708X-RAY DIFFRACTION100
4.848-40.94430.23281610.20622799X-RAY DIFFRACTION99

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