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- PDB-9i2y: Human DHODH in Complex with QC6352 -

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Basic information

Entry
Database: PDB / ID: 9i2y
TitleHuman DHODH in Complex with QC6352
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE / DHODH / QC6352 / Inhibitor
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / 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) / dihydroorotate dehydrogenase (quinone) activity / 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-type TIM barrel
Similarity search - Domain/homology
Chem-9DJ / ACETATE ION / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKraemer, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Human DHODH in Complex with QC6352
Authors: Kraemer, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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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)41,2048
Polymers39,8571
Non-polymers1,3477
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-24 kcal/mol
Surface area14410 Å2
Unit cell
Length a, b, c (Å)90.384, 90.384, 122.511
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 / DHOdehase / Dihydroorotate oxidase


Mass: 39856.535 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, 127 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-9DJ / 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid


Mass: 387.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#6: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.62 Å3/Da / Density % sol: 66.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 34% PEG 400 0.2 M KSCN 0.2 M NaBr 0.1M acetate pH 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.95→66.05 Å / Num. obs: 42816 / % possible obs: 100 % / Redundancy: 20.4 % / CC1/2: 0.99 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 21.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2978 / CC1/2: 0.716

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→66.05 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.328 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19805 2111 4.9 %RANDOM
Rwork0.1776 ---
obs0.17867 40632 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.95→66.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 90 120 2900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122847
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162746
X-RAY DIFFRACTIONr_angle_refined_deg1.321.6513860
X-RAY DIFFRACTIONr_angle_other_deg0.4481.5866302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.946526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13110468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
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_it1.8992.5081435
X-RAY DIFFRACTIONr_mcbond_other1.8932.5061434
X-RAY DIFFRACTIONr_mcangle_it2.8014.4921789
X-RAY DIFFRACTIONr_mcangle_other2.8064.4941790
X-RAY DIFFRACTIONr_scbond_it2.7752.8541412
X-RAY DIFFRACTIONr_scbond_other2.6682.8181405
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1385.0572060
X-RAY DIFFRACTIONr_long_range_B_refined6.01124.633119
X-RAY DIFFRACTIONr_long_range_B_other5.97924.193104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 116 -
Rwork0.24 3006 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: -2.7584 Å / Origin y: -36.4601 Å / Origin z: 10.9288 Å
111213212223313233
T0.0034 Å2-0.0021 Å2-0.0009 Å2-0.0476 Å2-0.0006 Å2--0.0061 Å2
L1.6039 °2-0.6702 °20.5712 °2-0.8742 °20.0545 °2--1.959 °2
S-0.0068 Å °-0.0634 Å °0.0241 Å °-0.0096 Å °-0.0139 Å °-0.0574 Å °-0.0567 Å °0.0702 Å °0.0208 Å °

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