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- PDB-8vhm: Structure of DHODH in Complex with Fragment 2 -

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Basic information

Entry
Database: PDB / ID: 8vhm
TitleStructure of DHODH in Complex with Fragment 2
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DHODH / OXIDOREDUCTASE / INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
: / ACETATE ION / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsShaffer, P.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Discovery of Alternative Binding Poses through Fragment-Based Identification of DHODH Inhibitors.
Authors: DeRatt, L.G. / Pietsch, E.C. / Cisar, J.S. / Jacoby, E. / Kazmi, F. / Matico, R. / Shaffer, P. / Tanner, A. / Wang, W. / Attar, R. / Edwards, J.P. / Kuduk, S.D.
History
DepositionJan 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: 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)41,34412
Polymers39,9851
Non-polymers1,35911
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.904, 90.904, 123.135
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: 39984.664 Da / Num. of mol.: 1 / Fragment: residues 29-395
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 , 7 types, 220 molecules

#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-A1AA1 / N-{4-[(R)-cyclohexyl(hydroxy)methyl]phenyl}acetamide


Mass: 247.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.6 Å3/Da / Density % sol: 65.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.8
Details: 0.10 M NaAcetate pH 4.8, 2.30 M (NH4)2SO4, 30% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.26→78.72 Å / Num. obs: 27268 / % possible obs: 96.9 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.103 / Net I/σ(I): 12.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.26-2.513.40.4962.4773340.8640.58597.9
2.51-2.770.21251080.9590.249
2.77-3.180.11150650.9840.13
3.18-3.880.05744100.9950.067
3.88-4.910.03927340.9980.046
4.91-6.310.04513870.9970.053
6.31-9.210.0368380.9980.042
9.21-14.740.0252970.9980.029
14.74-78.720.0279510.033

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→78.72 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1180 4.3 %RANDOM
Rwork0.196 ---
obs0.197 27268 96.9 %-
Displacement parametersBiso mean: 10.775 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.2 Å20 Å2
2---0.41 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.26→78.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 88 209 3070
LS refinement shellResolution: 2.26→2.32 Å
RfactorNum. reflection% reflection
Rfree0.564 88 4.3 %
Rwork0.445 1945 -
obs--98.1 %
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)
17.05110.09730.37061.3872-0.8882.5555-0.2506-0.6701-0.19960.61180.0359-0.44460.0790.50520.21460.62580.0327-0.09280.498-0.0720.3482-23.55824.07324.841
20.49790.1706-0.20881.8135-0.41191.604-0.02390.06020.0147-0.07620.0047-0.0257-0.01450.00330.01910.224-0.02040.0010.21580.00290.0012-34.84414.8587.705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 70
2X-RAY DIFFRACTION2A71 - 395

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