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- PDB-7df6: Mouse Galectin-3 CRD in complex with novel tetrahydropyran-based ... -

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Basic information

Entry
Database: PDB / ID: 7df6
TitleMouse Galectin-3 CRD in complex with novel tetrahydropyran-based thiodisaccharide mimic inhibitor
ComponentsGalectin-3
KeywordsCARBOHYDRATE / Galectin-3 Carbohydrate Recognition Domain / Inhibitor / Complex / Tetrahydropyran / Thiodigalactoside
Function / homology
Function and homology information


negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / 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 endocytosis / IgE binding / Fc-gamma receptor I complex binding ...negative regulation of cell proliferation in bone marrow / advanced glycation end-product receptor activity / positive regulation of serotonin secretion / 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 endocytosis / IgE binding / Fc-gamma receptor I complex binding / eosinophil chemotaxis / monosaccharide binding / negative regulation of T cell receptor signaling pathway / positive chemotaxis / macrophage chemotaxis / positive regulation of calcium ion import / monocyte chemotaxis / glial cell projection / immunological synapse / laminin binding / neutrophil chemotaxis / Neutrophil degranulation / extracellular matrix organization / extracellular matrix / RNA splicing / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / spliceosomal complex / mRNA processing / positive regulation of angiogenesis / collagen-containing extracellular matrix / cell differentiation / 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 / nucleus / 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
Chem-H5O / Galectin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGhosh, K. / Kumar, A.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Synthesis, Structure-Activity Relationships, and In Vivo Evaluation of Novel Tetrahydropyran-Based Thiodisaccharide Mimics as Galectin-3 Inhibitors.
Authors: Xu, L. / Hartz, R.A. / Beno, B.R. / Ghosh, K. / Shukla, J.K. / Kumar, A. / Patel, D. / Kalidindi, N. / Lemos, N. / Gautam, S.S. / Kumar, A. / Ellsworth, B.A. / Shah, D. / Sale, H. / Cheng, D. / Regueiro-Ren, A.
History
DepositionNov 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,5524
Polymers37,2782
Non-polymers1,2732
Water3,225179
1
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2762
Polymers18,6391
Non-polymers6371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2762
Polymers18,6391
Non-polymers6371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.140, 58.140, 130.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / IgE-binding protein / L-34 galactoside-binding lectin / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 18639.246 Da / Num. of mol.: 2 / Fragment: Carbohydrate Recognition Domain (CRD)
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-H5O / (2R,3R,4S,5R,6S)-2-(hydroxymethyl)-5-methoxy-6-[(3R,4R,5S)-4-oxidanyl-5-(4-pyrimidin-5-yl-1,2,3-triazol-1-yl)oxan-3-yl]sulfanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-3-ol


Mass: 636.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27F3N8O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.83 Å3/Da / Density % sol: 32.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris (pH 7.5-8.5), 0.4M NaSCN, 28-35% PEG 4000/6000

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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: 1.61→22.65 Å / Num. obs: 36334 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.082 / Rrim(I) all: 0.218 / Net I/σ(I): 8.2 / Num. measured all: 248791
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.61-1.656.91.3841838426470.7910.5611.4961.899.2
7.2-22.655.20.05624124640.9980.0280.06315.196.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CXB

7cxb


Resolution: 1.8→22.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.964 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1339 5.1 %RANDOM
Rwork0.19 ---
obs0.1933 24776 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.43 Å2 / Biso mean: 15.035 Å2 / Biso min: 4.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å20 Å2
2--0.4 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.8→22.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 136 180 2517
Biso mean--18.74 29.32 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0122363
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172149
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.7013217
X-RAY DIFFRACTIONr_angle_other_deg0.6651.5934987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4221.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13415383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7321519
X-RAY DIFFRACTIONr_chiral_restr0.10.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_rigid_bond_restr5.55134512
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 76 -
Rwork0.21 1778 -
all-1854 -
obs--99.3 %

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