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- PDB-7m41: Structure of TIM-3 in complex with N-(4-(8-chloro-2-methyl-5-oxo-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7m41 | ||||||
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Title | Structure of TIM-3 in complex with N-(4-(8-chloro-2-methyl-5-oxo-5,6-dihydro-[1,2,4]traizolo[1,5-c]quinazolin-9-yl)-3-methylphenyl)-1H-imidazole-2-sulfonamide (compound 38) | ||||||
![]() | Hepatitis A virus cellular receptor 2 | ||||||
![]() | IMMUNE SYSTEM / IgV | ||||||
Function / homology | ![]() 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 / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / toll-like receptor 7 signaling pathway ...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 / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / negative regulation of immunological synapse formation / positive regulation of interleukin-1 production / toll-like receptor 3 signaling pathway / 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 / mediator complex / macrophage activation involved in immune response / positive regulation of macrophage activation / anchoring junction / negative regulation of interleukin-2 production / negative regulation of NF-kappaB transcription factor activity / 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 non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / positive regulation of type II interferon 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 / negative regulation of gene expression / innate immune response / regulation of transcription by RNA polymerase II / cell surface / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rietz, T.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.9 KB | Display | ![]() |
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PDB format | ![]() | 46.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m3yC ![]() 7m3zC ![]() 5f71S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 12298.002 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: 2.18 Å3/Da / Density % sol: 43.66 % / Mosaicity: 0.827 ° |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 26, 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: 1.79→30 Å / Num. obs: 19569 / % possible obs: 97.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 11.73 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.034 / Rrim(I) all: 0.095 / Χ2: 2.031 / Net I/σ(I): 11.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5F71 Resolution: 1.79→26.91 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.22 / 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: 78.79 Å2 / Biso mean: 15.777 Å2 / Biso min: 3.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.79→26.91 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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