31NV | pdb_000031nv

Crystal structure of the complex of galectin-8N-TDG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 
    0.293 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Structural and Biophysical Characterization of C-Glycosylic 1,2-Thiodisaccharides Reveals Determinants of Selective Binding to Galectin-7 and Galectin-8N.

Tsagkarakou, A.S.Kantsadi, A.L.Theodoridou, V.I.Veliotis, N.Lazar, L.Jozsef, J.Juhasz, L.Kontopidis, G.Leffler, H.Nilsson, U.J.Somsak, L.Leonidas, D.D.

(2026) ChemMedChem 21: e70439-e70439

  • DOI: https://doi.org/10.1002/cmdc.70439
  • Primary Citation Related Structures: 
    31NP, 31NV, 31NW

  • PubMed Abstract: 

    Achieving isoform selectivity within the galectin family remains a central challenge in glycomimetic drug design due to the highly conserved architecture of their carbohydrate recognition domains. Here, we define the structural and thermodynamic basis of recognition of a series of C-glycosylic 1,2-thiodisaccharides targeting human galectin-7 and the N-terminal domain of galectin-8 (galectin-8N). Using an integrated approach combining fluorescence polarization, isothermal titration calorimetry, and high-resolution X-Ray crystallography, we establish a clear structure-activity relationship across the ligand series. Compound 17 emerges as the most potent galectin-8N ligand (K d  = 13 μM), outperforming thiodigalactoside, while compound 13 shows preferential binding to galectin-7, demonstrating tunable isoform bias. Structural analysis reveals a conserved anchoring mechanism in which the β-galactoside unit (Gly-1) drives affinity through a rigid hydrogen-bonding and π-stacking network, whereas the second sugar (Gly-2) modulates potency by adopting distinct orientations in galectin-specific extended binding sites. Notably, ligand binding converges on conserved motifs while leaving nonconserved regions unexploited, highlighting clear opportunities for structure-guided optimization. Collectively, this work establishes C-glycosylic thiodisaccharides as a robust platform for selective galectin targeting and provides actionable design principles for next-generation inhibitors.


  • Organizational Affiliation
    • Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.

Macromolecule Content 

  • Total Structure Weight: 36.21 kDa 
  • Atom Count: 1,283 
  • Modeled Residue Count: 147 
  • Deposited Residue Count: 317 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galectin-8317Homo sapiensMutation(s): 0 
Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens)
Explore O00214 
Go to UniProtKB:  O00214
GTEx:  ENSG00000116977 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00214
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
1-thio-beta-D-galactopyranose-(1-1)-beta-D-galactopyranose
B
2N/AN/A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free:  0.293 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.03α = 90
b = 39.194β = 107.483
c = 55.734γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release