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Yorodumi- PDB-7m63: Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m63 | ||||||
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Title | Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with IACS-70099 | ||||||
Components | Indoleamine 2,3-dioxygenase 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / IDO1 / Inhibitor / Enzyme / Complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / positive regulation of T cell apoptotic process / negative 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | ||||||
Authors | Leonard, P.G. / Cross, J.B. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of IACS-9779 and IACS-70465 as Potent Inhibitors Targeting Indoleamine 2,3-Dioxygenase 1 (IDO1) Apoenzyme. Authors: Hamilton, M.M. / Mseeh, F. / McAfoos, T.J. / Leonard, P.G. / Reyna, N.J. / Harris, A.L. / Xu, A. / Han, M. / Soth, M.J. / Czako, B. / Theroff, J.P. / Mandal, P.K. / Burke, J.P. / Virgin- ...Authors: Hamilton, M.M. / Mseeh, F. / McAfoos, T.J. / Leonard, P.G. / Reyna, N.J. / Harris, A.L. / Xu, A. / Han, M. / Soth, M.J. / Czako, B. / Theroff, J.P. / Mandal, P.K. / Burke, J.P. / Virgin-Downey, B. / Petrocchi, A. / Pfaffinger, D. / Rogers, N.E. / Parker, C.A. / Yu, S.S. / Jiang, Y. / Krapp, S. / Lammens, A. / Trevitt, G. / Tremblay, M.R. / Mikule, K. / Wilcoxen, K. / Cross, J.B. / Jones, P. / Marszalek, J.R. / Lewis, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m63.cif.gz | 194.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m63.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 7m63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/7m63 ftp://data.pdbj.org/pub/pdb/validation_reports/m6/7m63 | HTTPS FTP |
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-Related structure data
Related structure data | 7b1oC 7m7dC 5etwS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46295.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDO1, IDO, INDO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14902, indoleamine 2,3-dioxygenase #2: Chemical | 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: 2.71 Å3/Da / Density % sol: 54.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris pH 8.0, 18% (w/v) PEG6000, 0.2 M NaCl / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→52.63 Å / Num. obs: 18604 / % possible obs: 98.8 % / Redundancy: 13.8 % / Biso Wilson estimate: 70.6 Å2 / CC1/2: 0.536 / Rmerge(I) obs: 0.511 / Rpim(I) all: 0.146 / Rrim(I) all: 0.533 / Net I/σ(I): 6.4 / Num. measured all: 257586 / Scaling rejects: 2191 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ETW Resolution: 3.1→52.63 Å / SU ML: 0.8214 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.147 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 67.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→52.63 Å
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Refine LS restraints |
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LS refinement shell |
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