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- PDB-7m3z: Structure of TIM-3 in complex with N-(4-(8-chloro-2-mehtyl-5-oxo-... -

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Basic information

Entry
Database: PDB / ID: 7m3z
TitleStructure 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)
ComponentsHepatitis A virus cellular receptor 2
KeywordsIMMUNE 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 / 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
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-YQD / Hepatitis A virus cellular receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsRietz, T.A.
CitationJournal: 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
DepositionMar 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hepatitis A virus cellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7563
Polymers12,2981
Non-polymers4582
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.928, 85.168, 53.476
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-397-

HOH

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Components

#1: Protein Hepatitis A virus cellular receptor 2 / HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell ...HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell immunoglobulin mucin receptor 3 / TIM-3 / T-cell membrane protein 3


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
#2: Chemical ChemComp-YQD / N-{4-[(4S,10aP)-8-chloro-2-methyl-5-oxo-5,6-dihydro[1,2,4]triazolo[1,5-c]quinazolin-9-yl]-3-methylphenyl}methanesulfonamide


Mass: 417.869 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16ClN5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.38 % / Mosaicity: 0.247 °
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.427.20.41610790.9240.1650.4480.889100
1.42-1.4580.37510450.9490.140.4010.889100
1.45-1.4880.33410750.9590.1240.3570.923100
1.48-1.518.10.2910510.960.1080.311.021100
1.51-1.5480.26510520.9720.0990.2831.032100
1.54-1.5880.22310780.980.0830.2381.069100
1.58-1.628.10.18910600.9830.070.2021.168100
1.62-1.668.10.16410500.990.0610.1751.338100
1.66-1.718.10.1610680.9880.0590.171.346100
1.71-1.768.10.14310650.990.0530.1521.461100
1.76-1.838.10.12910700.9920.0470.1371.846100
1.83-1.98.10.10910700.9940.040.1161.957100
1.9-1.998.10.09110700.9960.0340.0972.012100
1.99-2.098.20.07810800.9960.0280.0831.909100
2.09-2.228.10.06510910.9970.0240.071.644100
2.22-2.398.10.06210690.9970.0230.0671.889100
2.39-2.638.10.05910880.9970.0220.0632.04100
2.63-3.028.10.04210980.9990.0150.0441.592100
3.02-3.880.0311100.9990.0110.0321.313100
3.8-307.50.02711750.9990.010.0291.27599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.49 Å26.74 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.8.3phasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F71

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
RfactorNum. reflection% reflection
Rfree0.1954 1006 4.67 %
Rwork0.1831 20517 -
obs0.1837 21523 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.02 Å2 / Biso mean: 17.7081 Å2 / Biso min: 6.29 Å2
Refinement stepCycle: final / Resolution: 1.4→26.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 29 139 1030
Biso mean--13.19 25.99 -
Num. residues----109
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.470.25531190.220729063025
1.47-1.570.26041320.200429143046
1.57-1.690.22141750.18628473022
1.69-1.860.23651560.185228983054
1.86-2.120.181450.17929283073
2.12-2.680.22461220.196229703092
2.68-26.740.16341570.16930543211

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