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- PDB-8ilu: Crystal structure of mouse Galectin-3 in complex with small molec... -

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Basic information

Entry
Database: PDB / ID: 8ilu
TitleCrystal structure of mouse Galectin-3 in complex with small molecule inhibitor
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Fibrosis / Galactose
Function / homology
Function and homology information


negative regulation of cell proliferation in bone marrow / NK T cell activation / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / oligosaccharide binding / negative regulation of NK T cell activation / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / cornified envelope ...negative regulation of cell proliferation in bone marrow / NK T cell activation / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / oligosaccharide binding / negative regulation of NK T cell activation / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / cornified envelope / regulation of T cell apoptotic process / mononuclear cell migration / receptor ligand inhibitor activity / signaling receptor inhibitor activity / Fc-gamma receptor I complex binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration / IgE binding / eosinophil chemotaxis / monosaccharide binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / regulation of T cell proliferation / monocyte chemotaxis / immunological synapse / glial cell projection / laminin binding / neutrophil chemotaxis / Neutrophil degranulation / extracellular matrix organization / RNA splicing / negative regulation of extrinsic apoptotic signaling pathway / skeletal system development / positive regulation of protein localization to plasma membrane / spliceosomal complex / molecular condensate scaffold activity / positive regulation of protein-containing complex assembly / extracellular matrix / mRNA processing / positive regulation of angiogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / carbohydrate binding / protein phosphatase binding / killing of cells of another organism / cell differentiation / mitochondrial inner membrane / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / THIOCYANATE ION / Galectin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, A. / Jinal, S. / Raman, S. / Ghosh, K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Bioorg.Med.Chem. / Year: 2024
Title: Identification of benzothiazole derived monosaccharides as potent, selective, and orally bioavailable inhibitors of human and mouse galectin-3; a rare example of using a S···O ...Title: Identification of benzothiazole derived monosaccharides as potent, selective, and orally bioavailable inhibitors of human and mouse galectin-3; a rare example of using a S···O binding interaction for drug design.
Authors: Liu, C. / Wang, W. / Feng, J. / Beno, B. / Raja, T. / Swidorski, J. / Manepalli, R.K.V.L.P. / Vetrichelvan, M. / Rao Jalagam, P. / Nair, S.K. / Gupta, A. / Panda, M. / Ghosh, K. / ...Authors: Liu, C. / Wang, W. / Feng, J. / Beno, B. / Raja, T. / Swidorski, J. / Manepalli, R.K.V.L.P. / Vetrichelvan, M. / Rao Jalagam, P. / Nair, S.K. / Gupta, A. / Panda, M. / Ghosh, K. / Kaushikkumar Shukla, J. / Sale, H. / Shah, D. / Singh Gautam, S. / Patel, D. / Mathur, A. / Ellsworth, B.A. / Cheng, D. / Regueiro-Ren, A.
History
DepositionMar 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-3
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1106
Polymers32,9102
Non-polymers1,2004
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area12950 Å2
Unit cell
Length a, b, c (Å)40.730, 49.600, 60.550
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Galectin-3 / Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / ...Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / IgE-binding protein / L-34 galactoside-binding lectin / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 16454.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lgals3 / Production host: Escherichia coli (E. coli) / References: UniProt: P16110
#2: Chemical ChemComp-Q1L / (2R,3R,4R,5R,6S)-2-(hydroxymethyl)-6-[2-(2-methyl-1,3-benzothiazol-6-yl)-1,2,4-triazol-3-yl]-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol


Mass: 559.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H20F3N7O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.85 Å3/Da / Density % sol: 33.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 30 % PEG 6K, 0.100M TRIS PH8.2, 0.400M NASCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.969 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.8→31.43 Å / Num. obs: 21379 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.847 Å / Num. unique obs: 1602 / Rrim(I) all: 0.206 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→31.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.956 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN TH INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1072 4.8 %RANDOM
Rwork0.164 ---
obs0.167 21379 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.22 Å2
2--0.53 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 82 193 2441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONr_bond_refined_d0.022327
X-RAY DIFFRACTIONr_bond_other_d040
X-RAY DIFFRACTIONr_angle_refined_deg2.1783174
X-RAY DIFFRACTIONr_angle_other_deg1.01486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.822281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.312108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.717374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1818
X-RAY DIFFRACTIONr_chiral_restr0.165350
X-RAY DIFFRACTIONr_gen_planes_refined0.0122080
X-RAY DIFFRACTIONr_gen_planes_other0.00114
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3161109
X-RAY DIFFRACTIONr_mcbond_other2.3131108
X-RAY DIFFRACTIONr_mcangle_it3.3551383
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9671218
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 75 -
Rwork0.206 1602 -
obs--100 %

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