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Yorodumi- PDB-7m3z: Structure of TIM-3 in complex with N-(4-(8-chloro-2-mehtyl-5-oxo-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m3z | ||||||
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Title | Structure of TIM-3 in complex with N-(4-(8-chloro-2-mehtyl-5-oxo-5,6-dihydro-[1,2,4]triazolo[1,5-c]quinazolin-9-yl)-3-methylphenyl)methanesulfonamdide (compound 35) | ||||||
Components | Hepatitis A virus cellular receptor 2 | ||||||
Keywords | IMMUNE SYSTEM / IgV | ||||||
Function / homology | Function and homology information regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of T-helper 1 type immune response / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of defense response to bacterium / toll-like receptor 7 signaling pathway / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of T-helper 1 type immune response / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of defense response to bacterium / toll-like receptor 7 signaling pathway / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / toll-like receptor 3 signaling pathway / negative regulation of immunological synapse formation / positive regulation of interleukin-1 production / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / toll-like receptor 9 signaling pathway / macrophage activation involved in immune response / mediator complex / positive regulation of macrophage activation / anchoring junction / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-2 production / positive regulation of interleukin-4 production / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / immunological synapse / maternal process involved in female pregnancy / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of type II interferon production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / cellular response to lipopolysaccharide / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / early endosome / defense response to Gram-positive bacterium / inflammatory response / innate immune response / negative regulation of gene expression / regulation of transcription by RNA polymerase II / cell surface / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Rietz, T.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Fragment-Based Discovery of Small Molecules Bound to T-Cell Immunoglobulin and Mucin Domain-Containing Molecule 3 (TIM-3). Authors: Rietz, T.A. / Teuscher, K.B. / Mills, J.J. / Gogliotti, R.D. / Lepovitz, L.T. / Scaggs, W.R. / Yoshida, K. / Luong, K. / Lee, T. / Fesik, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m3z.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m3z.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 7m3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m3z_validation.pdf.gz | 701.7 KB | Display | wwPDB validaton report |
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Full document | 7m3z_full_validation.pdf.gz | 703.1 KB | Display | |
Data in XML | 7m3z_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 7m3z_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/7m3z ftp://data.pdbj.org/pub/pdb/validation_reports/m3/7m3z | HTTPS FTP |
-Related structure data
Related structure data | 7m3yC 7m41C 5f71S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12298.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HAVCR2, TIM3, TIMD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDQ0 |
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#2: Chemical | ChemComp-YQD / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.38 % / Mosaicity: 0.247 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.8 M sodium tartrate dibasic dihydrate, 0.1 M HEPES pH 6.8-8.2, and 10 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 8, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→30 Å / Num. obs: 21544 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 12.15 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.021 / Rrim(I) all: 0.061 / Χ2: 1.437 / Net I/σ(I): 11.1 / Num. measured all: 172502 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 5F71 Resolution: 1.4→26.74 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.5 / 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: 56.02 Å2 / Biso mean: 17.7081 Å2 / Biso min: 6.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→26.74 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %
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