+Open data
-Basic information
Entry | Database: PDB / ID: 6lp8 | ||||||
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Title | Crystal structure of human DHODH in complex with inhibitor 1243 | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / DHODH / inhibitor | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Chen, Q. / Yu, Y. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Bifunctional Naphtho[2,3- d ][1,2,3]triazole-4,9-dione Compounds Exhibit Antitumor Effects In Vitro and In Vivo by Inhibiting Dihydroorotate Dehydrogenase and Inducing Reactive Oxygen Species Production. Authors: Zuo, Z. / Liu, X. / Qian, X. / Zeng, T. / Sang, N. / Liu, H. / Zhou, Y. / Tao, L. / Zhou, X. / Su, N. / Yu, Y. / Chen, Q. / Luo, Y. / Zhao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lp8.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lp8.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 6lp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lp8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6lp8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6lp8_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6lp8_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/6lp8 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/6lp8 | HTTPS FTP |
-Related structure data
Related structure data | 6jmdC 6jmeC 6lp6C 6lp7C 6j3bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 , 8 types, 294 molecules
#2: Chemical | ChemComp-FMN / | ||||||||||
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#3: Chemical | ChemComp-ORO / | ||||||||||
#4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-LDA / | #7: Chemical | ChemComp-B6O / | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: hepes pH4.6 2M AMMONIUM SULPHATE 30%Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 55261 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.033 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.79→1.83 Å / Num. unique obs: 3640 / CC1/2: 0.942 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J3B Resolution: 1.79→48.255 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.09 Å2 / Biso mean: 25.73 Å2 / Biso min: 6.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.79→48.255 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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