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- PDB-7e0q: Crystal Structure of Human Indoleamine 2,3-dioxygenagse 1 (hIDO1)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7e0q | ||||||
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Title | Crystal Structure of Human Indoleamine 2,3-dioxygenagse 1 (hIDO1) Complexed with (1S,2R)-2-(((6-Bromo-1H-indazol-4-yl)amino)methyl)cyclohexan-1-ol (22) | ||||||
![]() | Indoleamine 2,3-dioxygenase 1 | ||||||
![]() | OXIDOREDUCTASE / Indoleamine 2 / 3-dioxygenase 1 | ||||||
Function / homology | ![]() indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response ... indoleamine 2,3-dioxygenase / smooth muscle contractile fiber / indoleamine 2,3-dioxygenase activity / positive regulation of chronic inflammatory response / kynurenic acid biosynthetic process / tryptophan 2,3-dioxygenase activity / positive regulation of T cell tolerance induction / tryptophan catabolic process to kynurenine / stereocilium bundle / positive regulation of type 2 immune response / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / Tryptophan catabolism / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / swimming behavior / negative regulation of interleukin-10 production / multicellular organismal response to stress / T cell proliferation / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / female pregnancy / response to lipopolysaccharide / electron transfer activity / inflammatory response / heme binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, G.-B. / Ning, X.-L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray Structure-Guided Discovery of a Potent, Orally Bioavailable, Dual Human Indoleamine/Tryptophan 2,3-Dioxygenase (hIDO/hTDO) Inhibitor That Shows Activity in a Mouse Model of Parkinson's Disease. Authors: Ning, X.L. / Li, Y.Z. / Huo, C. / Deng, J. / Gao, C. / Zhu, K.R. / Wang, M. / Wu, Y.X. / Yu, J.L. / Ren, Y.L. / Luo, Z.Y. / Li, G. / Chen, Y. / Wang, S.Y. / Peng, C. / Yang, L.L. / Wang, Z.Y. ...Authors: Ning, X.L. / Li, Y.Z. / Huo, C. / Deng, J. / Gao, C. / Zhu, K.R. / Wang, M. / Wu, Y.X. / Yu, J.L. / Ren, Y.L. / Luo, Z.Y. / Li, G. / Chen, Y. / Wang, S.Y. / Peng, C. / Yang, L.L. / Wang, Z.Y. / Wu, Y. / Qian, S. / Li, G.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.7 KB | Display | ![]() |
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PDB format | ![]() | 127.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 39.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e0oC ![]() 7e0pC ![]() 7e0sC ![]() 7e0tC ![]() 7e0uC ![]() 5etwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44110.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% to 23% PEG 8000, 0.2M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Oct 29, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.46→71.31 Å / Num. obs: 36987 / % possible obs: 97.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 53.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Net I/σ(I): 19.4 / Num. measured all: 488084 / Scaling rejects: 3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5etw Resolution: 2.462→51.79 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.79 Å2 / Biso mean: 59.7314 Å2 / Biso min: 26.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.462→51.79 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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