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- PDB-9fdb: Co-crystal structure of Galectin-3 with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 9fdb
TitleCo-crystal structure of Galectin-3 with an inhibitor
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Inhibitor
Function / homology
Function and homology information


negative regulation of NK T cell activation / mononuclear cell migration / 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / mononuclear cell migration / 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / signaling receptor inhibitor activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / molecular condensate scaffold activity / mRNA processing / carbohydrate binding / protein phosphatase binding / : / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2025
Title: Discovery of Galactopyranose-1-carboxamides as a New Class of Small, Novel, Potent, Selective, and Orally Active Galectin-3 Inhibitors.
Authors: Zumbrunn, C. / Remen, L. / Sager, C.P. / Grisostomi, C. / Stamm, C. / Krusi, D. / Glutz, S. / Schmidt, G. / Nayler, O. / Iglarz, M. / Mac Sweeney, A. / Chambovey, A. / Muller, M. / Mueller, ...Authors: Zumbrunn, C. / Remen, L. / Sager, C.P. / Grisostomi, C. / Stamm, C. / Krusi, D. / Glutz, S. / Schmidt, G. / Nayler, O. / Iglarz, M. / Mac Sweeney, A. / Chambovey, A. / Muller, M. / Mueller, C. / Bourquin, G. / Meyer, S. / Huhn, E. / Cattaneo, C. / Vercauteren, M. / Gatfield, J. / Bolli, M.H.
History
DepositionMay 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3485
Polymers15,7011
Non-polymers6474
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-10 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.486, 57.886, 62.417
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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 / Galactoside-binding protein / GALBP / IgE-binding protein / L-31 / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 15701.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-A1IB3 / (2~{R},3~{R},4~{S},5~{R},6~{R})-~{N}-cyclopropyl-~{N}-(2-hydroxyethyl)-6-(hydroxymethyl)-3,5-bis(oxidanyl)-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-2-carboxamide


Mass: 472.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23F3N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Ammonium citrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→31.23 Å / Num. obs: 19897 / % possible obs: 87.2 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rrim(I) all: 0.151 / Net I/σ(I): 8.4
Reflection shellResolution: 1.45→1.53 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 995 / CC1/2: 0.503 / Rrim(I) all: 1.44

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→31.228 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.244 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.085
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2099 982 4.935 %
Rwork0.1802 18915 -
all0.182 --
obs-19897 87.161 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.736 Å20 Å20 Å2
2--2.47 Å2-0 Å2
3----1.734 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 42 85 1227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0121253
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161174
X-RAY DIFFRACTIONr_angle_refined_deg2.4351.8451714
X-RAY DIFFRACTIONr_angle_other_deg0.6661.762694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6125154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.593511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.23310200
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.5721062
X-RAY DIFFRACTIONr_chiral_restr0.0550.2180
X-RAY DIFFRACTIONr_chiral_restr_other0.0240.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
X-RAY DIFFRACTIONr_nbd_refined0.1930.2163
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.2994
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2557
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.216
X-RAY DIFFRACTIONr_nbd_other0.170.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.210
X-RAY DIFFRACTIONr_mcbond_it1.2951.235595
X-RAY DIFFRACTIONr_mcbond_other1.2721.228592
X-RAY DIFFRACTIONr_mcangle_it2.1572.207751
X-RAY DIFFRACTIONr_mcangle_other2.1592.209752
X-RAY DIFFRACTIONr_scbond_it1.5221.329658
X-RAY DIFFRACTIONr_scbond_other1.5211.328659
X-RAY DIFFRACTIONr_scangle_it2.4462.407959
X-RAY DIFFRACTIONr_scangle_other2.4452.406960
X-RAY DIFFRACTIONr_lrange_it13.84814.7811271
X-RAY DIFFRACTIONr_lrange_other13.84314.7791272
X-RAY DIFFRACTIONr_rigid_bond_restr1.31632427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4880.315130.3113210.31116710.7910.92619.9880.308
1.488-1.5290.315200.2696970.2716130.9460.94444.45130.261
1.529-1.5730.309520.25110210.25415580.9390.94968.87030.239
1.573-1.6210.273610.26613120.26715150.9290.9590.62710.255
1.621-1.6740.268750.24113720.24314870.9530.95997.310.223
1.674-1.7330.285640.22813720.23114540.9220.96798.7620.207
1.733-1.7980.207800.20212860.20213660.9740.9741000.178
1.798-1.8710.228690.18412730.18613420.9690.9811000.16
1.871-1.9540.164520.16112370.16112890.9840.9861000.14
1.954-2.0490.202830.15811520.16112350.9790.9871000.141
2.049-2.1590.196570.15111340.15211910.9770.9861000.137
2.159-2.290.166380.15910600.15910980.9810.9851000.147
2.29-2.4470.182600.179910.1710510.9790.9811000.158
2.447-2.6410.244560.1829370.1859940.9720.9899.89940.17
2.641-2.8910.207440.1818640.1839080.9780.9811000.176
2.891-3.2290.184400.1747930.1758330.9810.981000.179
3.229-3.7220.122340.1517040.157380.990.9861000.165
3.722-4.5430.22340.1466050.1496390.970.9871000.167
4.543-6.3570.201310.1674770.1695080.9850.9841000.2
6.357-31.2280.321190.2223070.2263260.9430.9641000.282

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